We excited to share "Seeing the Unseen", our lab's half-year collaboration with artists Tamara Anna Efrat & Shaul Cohen and curator Maya Dvash, translating microbial ecology into art. Join The Grand Opening : 📍 Trumpeldor Gallery, Beer Sheva 📅 29.10.26 🔗 lifewp.bgu.ac.il/wp/stu/?page_id=22

New preprint from our lab Statistical learning of bacterial growth in combinatorially constructed environments, led by brilliant PhD student Andrea Arrabal. www.biorxiv.org/content/10.6... We systematically study nutrient-nutrient interactions in bacterial growth under carbon-limiting conditions.

Designing microbial communities is hard, and making them perform specific functions is even harder. @oventurelli2.bsky.social lab show that ML + Bayesian optimization can identify the right fiber–microbe combinations. A proof of concept for rational microbiome-diet design. doi.org/10.1038/s415...

Designing fiber–gut microbiome interactions with active learning - Nature Chemical Biology

Dietary fibers are a primary energy source for gut bacteria and shape the composition and function of the microbiome. Now, an active learning approach integrating explainable machine learning, Bayesia...

doi.org

Excited that this is finally out, led by @jhuisman.bsky.social with Jeff Gore, combining experiments, theory and natural microbiome data! As salinity rises, diversity and individual species growth rates fall, yet community's overall growth stays robust: faster growers take over and keep it going.

Nature Microbiology@natmicrobiol.nature.com · last mo.

Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky

Can giving a microbial community MORE food options make it LESS diverse? New study says yes. Classic theory: more resources = more niches = more species co-exist. But in half their communities, diversity dropped instead, some strains just eat more when given options! www.nature.com/articles/s41...

Increased nutrient diversity can induce loss of microbial diversity through enhanced resource uptake - Nature Ecology & Evolution

Increasing nutrient diversity is expected to promote microbial diversity. This study shows that more complex environments can enhance resource uptake, intensify competition and lead to microbial biodi...

nature.com

The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...

Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome

Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of...

biorxiv.org

Understanding how complex ecosystems assemble is hard. Predicting their behavior from individual components alone? Much harder. @dsegre.bsky.social show that monoculture metabolic profiles are enough to predict coexistence and design stable multi-species consortia. doi.org/10.64898/202...

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

Synthetic microbial ecology aims at designing communities with desired properties based on mathematical models of individual organisms. It is unclear whether simplified models harbor enough detail to ...

doi.org

How to give a bad talk? Short and precise points by @itaiyanai.bsky.social on how to give a talk and present your ideas. Highly recommend saving this and reading it before your next presentation. www.nature.com/articles/s41...

Grab a coffee and enjoy reading up on CO metabolism in methanotrophs! Freshwater ANME (own work): www.nature.com/articles/s41... Marine ANME (@Orphan lab): www.nature.com/articles/s41... Big thanks to our collaborators at QUT! @sjmcilroy.bsky.social (Heyu/Andy/Gene!) @cuwelte.bsky.social

Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea - Nature Communications

Anaerobic methane-oxidizing archaea mitigate methane emissions in anoxic environments. Here, Egas et al. show that these microbes can also oxidize carbon monoxide, prompting re-evaluation of their cla...

nature.com

One mutation. 23 species. Total community reshuffle. A 4-yr synthetic bacterial community experiment shows a single species evolving antibiotic resistance was enough to flip the entire community's state. Great work all!! @teppo-h.bsky.social 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

🥁 NEW study @vheidrich.bsky.social et al. on oral and gut microbiome and #straintransmission is now published in @cellpressblue.bsky.social www.cell.com/cell-press-b... 👏 Kudos to all the authors and collaborators! [illustration by Betina Servaes] 1/n

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio

Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...

journals.asm.org

How ancient are the building blocks of animal sensory systems? Key components of animal sensory systems evolved before animals. We find that choanoflagellates possess diverse & spatially segregated TRP channels, pointing to ancient origins of sensory specialization. doi.org/10.64898/202...

Fascinating new science in @pnas.org! Turns out "aerobic" soil bacteria have a survival trick. When oxygen drops, they adapt by hybridizing fermentation with carbon storage to stay alive! Nature's resilience is unmatched. @greening.bsky.social www.pnas.org/doi/abs/10.1...

Aerobic soil bacteria adapt to hypoxia by hybridizing fermentation with carbon storage | PNAS

In soil ecosystems, aerobic bacteria survive oxygen deprivation (hypoxia) by entering nonreplicative persistent states. In contrast to the well-stu...

pnas.org

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface www.biorxiv.org/content/10.6...

Check out our pre-print led by the fantastic Massimo Amicone, collaborating with the Bollenbach lab! tinyurl.com/4h9p8mfb We build a simple intuition on how ecological interactions affect resistance evolution by expanding evolutionary rescue theory and testing it with two large sets of experiments

we got the cover!!! Novel light-driven schizorhodopsins from Antarctic Minisyncoccota (Patescibacteria) and cyanobacteria www.sciencedirect.com/science/arti...

Building all combinations of microbial strains used to require tedious work or pricey robotics. A new, rapid, low-cost method makes full factorial assembly accessible to any lab. Great work - Great impact! @asanchezlab.bsky.social elifesciences.org/articles/101...

Full factorial construction of synthetic microbial communities

A rapid, inexpensive, and easy to implement experimental protocol enables the construction of combinatorially complete sets of microbial consortia.

elifesciences.org

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

Managing microbial interactions in environmental biotechnology: can we scale interaction principles? @cp-trendsmicrobiol.bsky.social Review by @wenyugu.bsky.social (EPFL), Xiang-Yi Li Richter, and Dave Johnson at @eawag.bsky.social www.cell.com/trends/micro...

Managing microbial interactions in environmental biotechnology: can we scale interaction principles?

Microbial interactions hold vast potential for improving sustainability, including waste upcycling, greenhouse gas mitigation, contaminant bioremediation, and host performance. However, attempts to ma...

cell.com

Come and work with us in a beautiful corner of Germany: 5 years of funding for your microbiology research and lots of great colleagues 🦠🧫

Andreas Peschel @andreaspeschel.bsky.social · 4mo ago

You are an ambitious young scientist, on the verge to independence, in a research field related to our Cluster of Excellence @cmfi.bsky.social “Controlling Microbes to Fight Infections”? Join our vibrant, interactive scientific community in Tubingen. Repost and apply! www.nature.com/naturecareer...

Out Now! Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires #MicroSky

Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2Cayman enables computational analysis of carbohydrate-active enzymes (CAZymes) in microbial community data. It revealed novel mucus-foraging gut microorganisms and differences in gut microbial CAZyme repertoires associated with lifestyle and disease.

go.nature.com

Check our new preprint by Knopp M. et al.! Human gut microbiomes can impose strong +/- selection for resistant versions of resident opportunistic pathogens. In the case we follow up, selection is driven by altered carbohydrate utilisation that the resistant mutant evolves. doi.org/10.64898/202...

Out now in Nature Biotechnology! Alejandro González-Delgado and a fantastic team of collaborators worked across nine labs to get retron recombineering up-and-running in fifteen bacterial species. Molecular parts on addgene: www.addgene.org/browse/artic... Happy editing!

Nature Biotechnology@natbiotech.nature.com · 4mo ago

Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering - @seth-shipman.bsky.social @gladstoneinst.bsky.social go.nature.com/4tZluOU

"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule! Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other. www.nature.com/articles/s41...

Community context reshapes microbial proteomes and reduces functional overlap - Nature Microbiology

Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.

nature.com

Please remember that the International Symposium on Plasmid Biology (ISPB 2026) will take place 7–11 September 2026 in Berlin, Germany! A great opportunity to meet, reconnect, and engage with the global plasmid biology community. 🤝 plasmid-biology-2026.de

New benchmark by @tclavel.bsky.social & @treichelnicole.bsky.social reveals that while 0.5 Gb works for profiling, de novo MAG assembly requires >10 Gb. Crucially, they found that only 55-82% of high-quality MAGs accurately represented original strains. Full Article: doi.org/10.1038/s415...

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 accuracy of metagenomic analy...

doi.org

New paper out in Nature Comms 🎉 Congrats to first author @sekid.bsky.social & thanks team & collaborators We show that B. bifidum & E. coli can cooperate in the breastfed infant gut through nutrient cross-feeding, helping shape early-life microbiome development 🦠👶 www.nature.com/articles/s41...

Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum - Nature Communications

Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with...

nature.com

We found that TIR domains in animal immune proteins, including the human TLR4, are enzymes that cleave NAD+ to produce the signaling molecule cADPR Read our new preprint by talented Bohdana Hurieva: “Conserved catalytic activity of immune TIR domains in animals” www.biorxiv.org/content/10.6...

Interested in a *staff computational scientist* position? We are looking for an experienced computational biologist (ideally with microbiology experience) to support published packages while also driving new research. Pay range $73k-$111k w excellent benefits. careers.peopleclick.com/careerscp/cl...

Computational Biology Program Scientist

MIT - Computational Biology Program Scientist - Cambridge MA 02139

careers.peopleclick.com