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Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Co-abundance analysis of 938 healthy individuals uncovers how host factors shape gut microbiome interactions, highlighting a core set of 200 impacted genera and additional factor-specific interactions...

Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...

Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

Abstract. Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most curre

Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...

Nature Reviews Microbiology, Published online: 23 July 2025; doi:10.1038/s41579-025-01205-7Lactobacilli are important members of human, animal and insect microbiomes and are prominent in food fermentations. In this Review, Mejía-Caballero and Marco explore the diversity of lactobacilli, focusing on their fundamental traits and their applications in foods and medicine.