A journey through the microbiome, shaped by growth and support | EMBL

EMBL alumna Lisa Maier, recipient of the 2026 John Kendrew Award, discusses her scientific achievements, the importance of science engagement, and how she carries on the ‘EMBL spirit’

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Impacts of pollution on the soil microbiome - Nature Reviews Microbiology

In this Review, Zhu and colleagues overview the major types of soil pollution in the Anthropocene and their effects on soil microbiome composition, function and dynamics, while also exploring microbio...

nature.com

Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance - Nature Communications

Antibiotic resistance can evolve through the combination of factors but the predictability of this is unclear. Here, the authors used high-throughput evolution experiments to reveal that antibiotic re...

nature.com

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens

Author summary Bacteriophages, or phages, are viruses that infect bacteria and play central roles in shaping microbial communities across ecosystems. Despite their ecological importance, the bacterial...

journals.plos.org

Designing fiber-gut microbiome interactions with active learning

Agus, A., Clément, K. & Sokol, H. Gut microbiota-derived metabolites as central regulators in metabolic disorders. Gut 70, 1174–1182 (2021). Rinninella, E. et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms 7, 14 (2019). Das, B. & Nair, G. B. Homeostasis and dysbiosis of the gut microbiome in health and disease. J. Biosci. 44, 117 (2019). Schult, D. et al. Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19. Gut Microbes 14, 2031840 (2022). He, Y. et al. Effects of dietary fiber on human health. Food Sci. Hum. Wellness 11, 1–10 (2022). Tanes, C. et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe 29, 394–407 (2021). Cantu-Jungles, T. M. & Hamaker, B. R. New view on dietary fiber selection for predictable shifts in gut microbiota. mBio 11, e02179-19 (2020). Oliver, A. et al. High-fiber, whole-food dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids. mSystems 6, 10–1128 (2021). Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Bäckhed, F. From dietary fiber to host physiology: short-chain fatty acids as...

nature.com

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00

biorxiv.org

The microbial unknome, a repertoire for microbial chatting? - Heredity

Heredity - The microbial unknome, a repertoire for microbial chatting?

nature.com

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

Scientists show how sweeteners slow the growth of certain gut bacteria

Cambridge researchers have shown how commonly-used sweeteners slow the growth of certain gut bacteria.

news-medical.net

Metabolic processes shape microbial interaction distributions

Microbial communities are largely driven by metabolic interactions, whereby species compete for shared resources and exchange byproducts. Such interactions are commonly classified by their sign alone....

biorxiv.org

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

Engineering commensal microbes for host health

Engineered live biotherapeutic products (eLBPs) are emerging as a promising therapeutic class for a diverse range of diseases. Advances across the field have revealed core design principles, including...

cell.com

OpenEvo: An Open-Source Platform for Automated Evolution and Analysis

Here we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-s...

biorxiv.org

High-throughput DNA engineering by mating bacteria

Matsui et al. introduce SCRIVENER, an in vivo DNA assembly platform that stitches DNA blocks together by mating bacteria. The method enables scalable construction and verification of long DNA molecule...

cell.com

A conceptual framework to dissect emergent functions in microbial communities

Microbial communities play vital roles in diverse ecosystems and are key drivers of numerous industrial or health-related applications. In many cases,…

sciencedirect.com

The Novo Nordisk Foundation Prize

Our prizes are awarded to researchers who have contributed to scientific breakthroughs or in other ways distinguished themselves within natural or medical science.

novonordiskfoundationprize.com

Identification of chemical features for improved outer membrane permeation in mycobacteria using machine learning

Nature Microbiology, Published online: 30 June 2026; doi:10.1038/s41564-026-02412-5Screening 1,572 compounds for mycomembrane permeation plus cheminformatic and machine learning analyses reveals features associated with improved permeation in the pathogen Mycobacterium tuberculosis and model organism M. smegmatis.

go.nature.com

CarveMe-GutMicrobes: Automated Metabolic Model Reconstruction for Gut Microbial Species and Communities

Genome-scale metabolic models (GSMMs) are important aids towards system-level understanding of the metabolic physiology of the gut microbes and for rational microbiome engineering. While large-scale r...

biorxiv.org