Context-Dependent Metabolic Adaptation in Microbial Communities: From Monocultures to Complex Ecological Interactions https://www.biorxiv.org/content/10.1101/2025.10.22.683057v1

In a break from recent themes & in honor of World Phage Week (Oct 22-28), some reflections on the world of bacteria and phage, part of a short series explaining the rationale for why we have invested so much time in exploring when microbes get sick too. joshuasweitz.substack.com/p/happy-worl...

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

How exercise promotes the immune system vs cancer, working through a gut bacteria metabolite www.cell.com/cell/abstrac...

It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in therapy. What would need to change? Researcher Alexander Harms explains. ethz.ch/en/news-and-...

Excited to highlight our News & Views on the article by Torres et al. from @delafuentelab.bsky.social team 🚀 Archaea could help to discover new antibiotics! Read it here: www.nature.com/articles/s41...

Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology. www.nature.com/articles/s41...

Deep-mining the archaeal proteome for antibiotics News & Views by Rafael Laso-Pérez @gecko1990.bsky.social @delafuentelab.bsky.social Read it here: rdcu.be/eHNwa

Excellent work done by Borja, Miguel, and Kostas! Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them academic.oup.com/ismecommun/a...

A new work on how context matters... from the PhD Thesis of Rodrigo the Great

Happy to share our upcoming paper on pioneer microbial communities, including viruses, establishing after glacier retreat, result of a great collaboration @ua.es @mncn-csic.bsky.social @univgirona.bsky.social @pepa-anton.bsky.social @estherrubioport.bsky.social academic.oup.com/ismecommun/a...

🦠➡️🧬 Community context matters! In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution. Check out the preprint 👇🏼

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

(1/5)For over a century, the hunt for new antibiotics has focused almost exclusively on bacteria and fungi. Today, that paradigm shifts. By coupling state-of-the-art AI with the vast, largely uncharted diversity of Archaea, we open a new frontier for molecular discovery.

Check out the new paper of my former lab about novel haloviruses infecting Haloquadratum walsbyi, the "square queen archaeon" of hypersaline systems 👑🟪 academic.oup.com/ismej/advanc...

Seeing this published is even better than eating sweets! I am so happy and proud of whole @lisamaierlab.bsky.social, especially Lisa and @jdlcz.bsky.social who walked the funny/exciting/rocky road with me until the very end. Check it out! #science #microbiome #health www.nature.com/articles/s41...

Kicking off my account with great news🎉: our latest paper on extracellular vesicles from human gut archaea is out in @natcomms.nature.com with @mkrupovic.bsky.social and @sgribaldo.bsky.social! Published in parallel with the work of our colleagues from the Moissl-Eichinger Lab @chmoei.bsky.social🧵

Well done to Cortés Martin et al #phage #gut #Bacteroides #CrAss link: www.tandfonline.com/doi/full/10.... @uccresearch.bsky.social

Looking for a postdoc position in microbial aquatic ecology? Apply!!!

#phage #phagesky #microbiomesky

It’s Thursday! Episode #91 of #MattersMicrobial is up. Dr. Emily Davenport of Penn State joins the #QualityQuorum to discuss how host genetics impacts the microbiome. Please spread the #GoodMicrobialWord! @microbe.tv @asmicrobiology @univpugetsound youtu.be/5c7lxC1mHxk?...

Officially published! 🧬🦠 What if more phages didn't mean more death? We show that even strictly lytic phages can stabilize host populations via persistent, episomal infections (often referred to as pseudolysogeny). It's time to move beyond the lysis/lysogeny binary. #phagesky #microsky

🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...

"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors” www.science.org/doi/10.1126/...

To restore the gut microbiome after antibiotics, the right diet (rich in carbohydrates, low in fat) was a better approach than fecal microbial transplants (in the experimental model) www.nature.com/articles/s41... www.nature.com/articles/d41...

Here we share thoughts on next-gen cultivation: rdcu.be/ejPSb. Hope it helps 😄 Was fun to write with great colleagues @lisamaierlab.bsky.social @jselkrig.bsky.social @baerboletta.bsky.social @typaslab.bsky.social @mmmicrobiomelab.bsky.social @leibniz-dsmz.bsky.social @westermannlab.bsky.social

I am thrilled to share the first manuscript from the Wiles lab! We present "Phollow", an in vivo phage-tagging approach that enables direct observation of phage outbreaks with single-virion resolution by live imaging. Here some highlights 👇 www.nature.com/articles/s41...

A Review in Nature Medicine summarizes recent and compelling examples of microbiome-based interventions that are ripe for clinical adoption while also discussing the challenges and opportunities facing the field. go.nature.com/42LUmrU 🔒

Latest findings on cryptic infection of giant viruses published in @ScienceMagazine. We discovered a large virus hiding within a green algal genome producing virions. www.science.org/doi/10.1126/...

Thrilled to share the first part of my PhD, published today in The ISME Journal! A wonderful collaboration with Akash Arani (co-first author), @joshuasweitz.bsky.social , and @mkrupovic.bsky.social . Huge thanks to my mentors Fer and Pepa for their constant support. Let’s keep going! #phage

Can expression of a peptide lead to antimicrobial resistance? Yes it can! We discovered this for a toxin we work with and started exploring how #peptides, #antimicrobialresistance and de-novo gene birth can come together. @cp-trendsmicrobiol.bsky.social Amazing work by @rianneprins.bsky.social

These are the power numbers behind the fastest ever Tour of Flanders bit.ly/42oSRP8

🦠🌍 When did bacteria learn to breathe? A new study reconstructs 4 billion years of bacterial evolution. Surprisingly, some aerobic bacteria evolved before the Great Oxidation Event – oxygen tolerance may have paved the way for photosynthesis. 🔗 www.science.org/doi/10.1126/... #SciComm 🧪

New paper! We analyzed gut #microbiomes of 250+ individuals (ages 19–109). #Centenarians often show a high-methanogen “human cow” phenotype 🐄, with #Methanobrevibacter smithii dominance and youth-like archaeal profiles. #Archaea may stabilize networks in aging. Link: rdcu.be/egk03 @archaeasky

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New online! Genetics, ecology and evolution of phage satellites

🔬🦠 How to make sense of the taxonomic complexity & interpersonal variability of the gut microbiota? We propose that beneath this complexity lies a hierarchy of factors that control gut microbiota assembly. Read more! #Microbiome #GutHealth authors.elsevier.com/a/1km32_,2Ci...

In my first Drosophila study at @salehlabparis.bsky.social, we found that: 1. Enteric viral infections accelerate aging. 2. Even if the infection is cleared, aging process remains triggered. 3. Accelerated aging correlates with reduced lifespan. 📑Preprint: www.biorxiv.org/content/10.1...

Twists, turns and jumps: T6SS evolution within species @cp-trendsmicrobiol.bsky.social SpotLight on @naturecomms.bsky.social paper by @tonihabich.bsky.social et al from Daniel Unterweger lab at @mpi-evolbio.bsky.social www.cell.com/trends/micro...

Awesome! Congrats to Jesús et al 👏🏼

Viruses of "nanos" rules. Looking forward to reading it! @mkrupovic.bsky.social

Upcoming wastewater virome webinar from Dr. Mike Tisza, Feb. 12! Free for everyone. More: coms.osu.edu/events/early... #virus #virome #viromics #pathogen #sequencing #microbiome #microbe #bacteria #science #microbiology #webinar

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

No one realises just how crucial mitochondrial function is to longevity... The quality of your mitochondria determines how well every cell in your body functions. It's the unsung hero responsible for:

OUT NOW - Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection www.nature.com/articles/s41...

There are 2 common themes I see when athletes begin to build thier aerobic base: 1. It will take a lot of time 2. You need to go slower True aerobic gains can take months-years, not weeks. Set your season up for success by taking enough time to build your base.

The gut microbiome signature from different diets in 20,000 individuals. Red meat intake correlated with reduced cardiometabolic health; the opposite for plant-based foods or in omnivores with enriched plant-based intake www.nature.com/articles/s41...

Persistent virulent phages exist in bacterial isolates www.biorxiv.org/content/10.1... #jcampubs

To get 2025 off to a good start, I'm delighted to share with you our study published today in @naturemicrobiol.bsky.social 🎉 We studied the ability of the receptor-binding proteins (RBP) of >100 animal viruses to mediate entry into human cells. A short thread below. www.nature.com/articles/s41...