Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome. biorxiv.org/content/10.110… #biorxiv_micrbio

So happy that I can finally share the results of my first postdoc paper with Michael Baym!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! Here’s a photo of plasmids competing inside cells in a colony (1/n)

Gut3Gel: A High Throughput Mucus Model for Culturing Human Intestinal Microbiota biorxiv.org/content/10.110… #biorxiv_micrbio

Residence Time Structures Microbial Communities Through Niche Partitioning onlinelibrary.wiley.com/doi/10.1111/el…

Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes nature.com/articles/s4155…

Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats nature.com/articles/s4146…

Our paper on gut bacterial competition is out Cell Host & Microbe. Another very cool D-BIOL @ ETH Zurich & Universität Zürich collaboration with fantastic colleagues and friends involved. Huge thanks to Swiss National Science Foundation NCCR Microbiomes & EMBO Fellows for the continuous support. cell.com/cell-host-micr…

Bacteria exploit viral dormancy Temperate vs lytic phage present 2 opportunities for CRISPR-Cas immunizations 1.immunizations occur when phages choose lysogeny 2.memories acquired from prophages already in clonal population ➡️curing Modell Johns Hopkins Medicine cell.com/cell-host-micr…

A study by the Hardt lab, with the Sauer and von Mering labs, shows that sugars are abundant in the gut and drive Salmonella Typhimurium expansion across murine models. nature.com/articles/s4146…

Thrilled to share our latest publication in Nature Reviews Genetics! We explore how deep learning models infused with prior pathway knowledge — aka 'visible neural networks' — promise better predictive accuracy & interpretability in multi-omics data analysis. nature.com/articles/s4157…

Coexistence Theory for Microbial Ecology, and Vice Versa …icro-journals.onlinelibrary.wiley.com/doi/10.1111/14…

Machine learning for optimal growth temperature prediction of prokaryotes using amino acid descriptors biorxiv.org/content/10.110…

📢 NIH BioArt Source, a free science and biomedical art resource library, offers an array of high-quality illustrations, vectors, & brushes, free to use & download. See the full catalog of free science and #biomedical illustrations: bioart.niaid.nih.gov #FreeResource

Thrilled to share our new preprint on finer and flexible marker selection for microbial phylogenomics. Well done Henry Secaira and Xiaofang Jiang. Given any input genomes and an arbitrary number, it will find useful markers. Effective with incomplete MAGs. biorxiv.org/content/10.110…

Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes biorxiv.org/content/10.110… #biorxiv_micrbio

Ultrafast and accurate sequence alignment and clustering of viral genomes | Nature Methods nature.com/articles/s4159…

Gut bacteria and acetate team up to cut fat in mice without muscle loss #GutMicrobiome #SCFAs medicalxpress.com/news/2025-05-g…

Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests biorxiv.org/content/10.110…

Unraveling plankton adaptation in global oceans through the untargeted analysis of lipidomes science.org/doi/10.1126/sc…

Pathogen emergence is a complex and rare phenomenon Out of >40,000 named bacterial species only a fraction can cause disease in humans What leads to this quantum leap? In our recent paper PNASNews we decided to investigate this puzzling conundrum. pnas.org/doi/10.1073/pn…