New preprint w/Milena Chakraverti-Wuerthwein with Alissa Domenig. “Everything is everywhere; the environment selects.” But which traits does the environment select on? Is there a relationship between evolutionary conservation of traits and variation in community composition? doi.org/10.64898/202...

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

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...

Big congrats to our colleague @krukowskihubert.bsky.social on the Nature Microbiology paper linking gut transit time and diet to CKD microbiome changes. Another step in microbiome research!🧫 www.nature.com/articles/s41...

Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function - Nature Microbiology

A covariate-aware analysis reveals that microbiome changes in the gut of patients with chronic kidney disease are better explained by intestinal transit time than by kidney function.

nature.com

Happy to share the latest perspective piece from our lab! www.sciencedirect.com/science/arti...

Structuring complexity by mapping the possible in microbial ecosystems

Microbial ecosystems consist of many interacting components that integrate through stochastic and highly dynamic processes across multiple scales. Yet…

sciencedirect.com

Very cool phage study from @jeremyjbarr.bsky.social's lab. Isolation, engineering and ecology of temperate phages from the human gut #microbiomesky #phagesky

Isolation, engineering and ecology of temperate phages from the human gut - Nature

Human host-associated cellular products may act as induction agents for bacteriophages.

nature.com

Over the last year, Nature’s Careers team has been tapping into its global community of readers, writers, friends and colleagues to compile a list of laboratory hacks to help make scientists’ working lives easier. Here’s a list of 99 of those hacks. #Academicsky 🧪

These 99 'lab hacks' will make your scientific work easier

Nature asked contributors, editors and working researchers to share their best advice for scientists.

go.nature.com

We want to build models that help us understand how biological systems work. And for that, we need scientists who live at the interface of machine learning and biology. We’re recruiting Group Leaders! https://tinyurl.com/y35m6khy Call closes June 14th

Manu Prakash practices “recreational biology,” a scientific approach that explores life in the same playful way that puzzles probe math. “Basic science is not at the service of something, but the groundwork that is our entire society’s foundation.” www.quantamagazine.org/how-paradoxi...

How Paradoxical Questions and Simple Wonder Lead to Great Science | Quanta Magazine

Manu Prakash works on the world’s most urgent problems and seemingly frivolous questions at the same time. They add up to a philosophy he calls “recreational biology.”

quantamagazine.org

New online! Microorganisms thriving together as communities

Microorganisms thriving together as communities

Nature Reviews Microbiology, Published online: 29 May 2025; doi:10.1038/s41579-025-01199-2This Genome Watch article discusses the dominance of uncultivated microorganisms in natural ecosystems and how the consequent genome-driven insights could guide the rational design of synthetic microbial communities.

nature.com

Does publishing serve science or is science serving publishing? Damian Pattinson and I (@elife.bsky.social) argue scientific publishing has evolved into a system that, rather than facilitate scholarly communication, distorts and dictates it. onlinelibrary.wiley.com/doi/10.1002/... #OpenScience