Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.

Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

The impacts of microbiology on the storage of CO2 are poorly understood but could be critical to its safe geological disposal. We review evidence for microbial risks and opportunities, and argue for ...

Some metagenome assembled genome (MAG) datasets are not available in the standard locations (NCBI / ENA / etc) for a variety of reasons. Here you can contribute new ones you come across. To be recorde...

PhD Out of order: investigating genetic and environmental drivers of genome rearrangement (LANGRIDGE_Q26DTP) 2026/27 | UEA

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefi...

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

PhD Project - Linking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia, listed on FindAPhD.com

In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Background Long-read sequencing has revolutionised metagenomics through improved metagenome assembly, taxonomic classification and functional characterisation. Automation can enhance the throughput, reproducibility, and accuracy of library preparation. However, the validation of automated library preparation protocols remains undetermined for metagenomic workflows, which are particularly sensitive to methodological perturbation. Here, we compare long-read metagenomic sequencing of environmental samples through parallel manual and automated protocols. Results Although automated library preparation led to minor reduction in read and contig lengths, taxonomic classification rate and alpha diversity was slightly higher than manual libraries, including the detection of more rare taxa. Despite this, no significant difference in microbial community structure was identified between manual and automated libraries. Conclusions Despite minor differences in sequencing and classification metrics, automated and manual library preparation resulted in comparable characterization of environmental community metagenomes. These findings demonstrate the suitability of automation for high-throughput long-read metagenomics, with broad applicability to automated long-read sequencing for improved efficiency and reproducibility.