Here the authors propose guidance on the process of establishing a state-of-the-art collection of microorganisms, including project planning, strain deposition and the naming of new taxa.

Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...

The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

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’

Nature Microbiology, Published online: 23 July 2026; doi:10.1038/s41564-026-02414-3Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to tobramycin during chronic lung infection within patients.

All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...

A hub-based conference on Microbial Ecology and Evolution

Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious

Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…

Eriksson et al. conduct a global marine microbiome diversity analysis and demonstrate how the surface ocean latitudinal diversity gradient is disproportionately shaped by a few species-rich taxa. Mask...

High-level declarations pledging not to misuse metrics in research assessment are important, but they are far from enough. Senior academics, in particular, must use their influence to ensure instituti...

Nature Genetics - Peer Bork (1963–2026)

Ni et al. show that epigenetic phase variation (ePV)—gene expression changes mediated by bacterial DNA methylation—is prevalent in the human gut microbiome and associated with fluctuating environments...

Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174

Over three decades, rapid expansion of the transposable element ISL3 has reshaped Enterococcus faecium, which helps to explain this pathogen’s growing clinical threat.

In academia, the intersection of the postdoctoral stage, usually highly unstable and decisive to secure a permanent position, and motherhood, is the most prominent culprit of the well-known problem of the decreasing number of female researchers in senior academic positions. The loss of postdoctoral women from the academic path represents an unsustainable loss of talent, leading to unbalanced academic institutions where this phenomenon eventually gets perpetuated. The motherhood challenges for postdoctoral women begin from the moment they plan on getting pregnant and continue well after reincorporation to work after maternity leave. Here, we provide 10 actionable rules for these postdoctoral women approaching motherhood to increase their chances of remaining in the academic career. These rules will help postdoctoral women prepare for the challenge of becoming a mother while working towards their long-term academic goals, and establish a successful relationship with their supervisors and collaborators under the new circumstances. These rules should be complemented by the general effort from colleagues, supervisors, institutions, and academia as a whole, to create a more supportive working environment. It is in the utmost interest of the academic community to improve the retention of postdoctoral mums and promote their progression to more senior positions.

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...

Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...

van der Burg et al., (2026). Introduction to deep learning: Carpentries-style hands-on lesson material for introducing researchers to deep learning. Journal of Open Source Education, 9(95), 307, https...

Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol