Recent changes in Genentech’s scientific organization, occurring as the company makes artificial intelligence (AI) increasingly central to its research strategy, highlight a broader question facing bi...

Researchers are racing to culture a menagerie of exotic organisms and finding lots of surprises along the way.

0.12.0 — faster on both architectures, a faster --meth, and a large safety pass A broad optimization release that speeds up both Arm and x86 (unlike 0.11.0, which concentrated on Arm), plus a methy...

The 16S rRNA gene has - and continues to - play an important role in microbiology. It’s universality across prokaryotes and variation across species has allowed the sequencing of its hypervariable reg...

Biological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.

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...

Wastewater treatment relies on complex microbial communities, yet existing genome-resolved references for this essential engineered ecosystem remain dominated by short-read assemblies, limiting genome...

Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite pro...

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

In this paper, we study how well humans can detect text generated by commercial LLMs (GPT-4o, Claude, o1). We hire annotators to read 300 non-fiction English articles, label them as either human-writt...

A grounded take from the messy middle of an AI revolution

Nature Reviews Microbiology, Published online: 08 May 2026; doi:10.1038/s41579-026-01299-7In this Review, Vasse and Velicer explore the phylogenetic and functional diversity of predators of microorganisms, conceptualizing the forms of microbial predation along gradients, including gradients of evolutionary adaptedness for predation and privatization of prey-derived nutrients.

Genes involved in the biosynthesis of microbial natural products (NPs) are typically arranged in biosynthetic gene clusters (BGCs). Different congeners of an NP family typically possess distinct chemical features introduced by additional tailoring enzymes encoded in the corresponding BGC variants. However, tools to rapidly visualize the core gene set and distinguish it from variant-specific tailoring genes (VSTGs) in these BGCs are lacking. Here, the software tool BisCEET (Biosynthetic Cluster Environment Examination Tool) was developed, allowing comparison and visualization of the gene composition of related BGCs, thereby streamlining the identification of VSTGs in uncharacterized BGC variants and strains likely to produce novel NP congeners. The use of BisCEET is exemplified by analyzing bacterial BGCs of staurosporine-like indolocarbazoles and xantholipin-like polyketides, which enabled the identification of numerous apparent BGC variants. We anticipate that BisCEET will become a valuable bioinformatic asset, streamlining the prioritization of BGCs and the cultivation of microbial strains for the discovery of distinct NP variants and novel tailoring enzymes.

Failure is part and parcel of research, but discussing it sometimes seems to be taboo in science. It doesn’t need to be.

Do you want to lead the development of bioinformatics infrastructure for a state-of-the-art research laboratory dedicated to exploring the amazingly abundant and diverse life of environmental microorg

Escherichia coli ABC transporter-dependent capsule gene analysis alongside the development and application of the kTYPr in silico capsule typing tool uncovers E. coli capsule diversity across environm...

Extracellular DNA (eDNA) plays crucial roles in biofilm formation and function, yet the role of bacteriophages (phages) in controlling eDNA synthesis, structure and activity remains obscure. Here, we ...

Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil

AbstractProkaryotes form multicellular structures under both natural and experimental conditions, based on developmental programs that sometimes echo those known from eukaryotes. Recent research has i...

Nature Reviews Microbiology, Published online: 30 March 2026; doi:10.1038/s41579-026-01303-0This Genome Watch article explores how taking into account known phylogenetic relationships can improve computational efficiency for genomics, enabling improved genome data compression and faster sequence search as datasets continue to expand.