The maternal gut microbiome is a predictor of infant eczema.

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

Workshop at the Banff International Research Station in Banff, Alberta between Feb 8 and Feb 13, 2026: New Mathematical Theory in Eco-Evolutionary Modelling of Host-Symbiont Communities.

New study provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to infants’ gut microbiomes.

Most conversations about breast milk tend to focus on topics like nutrients, antibodies and bonding time rather than bacteria.

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.

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.

Over the past decades, medication use has steadily increased worldwide, with individuals frequently taking multiple medications (polypharmacy), often repeatedly over extended periods of time (1). Yet,...

IntroductionHuman breast milk is a sophisticated and complex biological fluid that provides crucial nutritional, immunological, and microbial benefits to inf...

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.

Growing insight into microbial symbioses highlights the need to model these systems mathematically. We discuss three areas requiring theoretical advancement: nested ecology within a host or holobiont,...

Growing insight into microbial symbioses highlights the need to model these systems mathematically. We discuss three areas requiring theoretical advan…

Cataloguing Earth's biodiversity remains one of biology's most formidable challenges, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing census of...

Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...

Background Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characteriz...

Background Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characteriz...

In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...

In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

Nature Reviews Genetics, Published online: 04 June 2025; doi:10.1038/s41576-025-00849-8In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.

ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal information associated with e...

Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...

Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...