The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome

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...

doi.org

The End of Disease

science.org

From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments

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

doi.org

home | GlobDB

globdb.org

Archaeal genes code for GGDEF domain proteins with diguanylate cyclase activity

ecoevorxiv.org

The elusive resistome: a global comparison reveals large discrepancies among detection pipelines

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

biorxiv.org

People who frequently use ChatGPT for writing tasks are accurate and robust detectors of AI-generated text

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...

arxiv.org

Seven points on the current state of AI in genomics

A grounded take from the messy middle of an AI revolution

blekhman.substack.com

Predation in microbial communities: gradients of nutritive killing

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.

dlvr.it

BisCEET: A Visual Browser for Biosynthetic Gene Clusters Aiding in the Identification of Natural Product Variants and Distinct Tailoring Enzymes

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.

pubs.acs.org

We need to talk about failure in science

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

nature.com

Bioinformatics Engineer in Microbial Single-Cell Genomics

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

aau.varbi.com

In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules - Nature Microbiology

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...

nature.com

Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms

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 ...

biorxiv.org