ArticleNature microbiology2025
Longitudinal phage-bacteria dynamics in the early life gut microbiome.
Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Nationwide cohort study reveals low bifidobacteria and distinct microbiota composition and function in Swedish newborns.Gut microbes · 2026Observational
- Classroom microbiome signatures of pest management associate with reduced asthma symptoms.The Journal of allergy and clinical immunology · 2026Article
- Bacteriophages as Phagobiotics: Scientific Rationale and Translational Boundaries for Gut Microbiome Modulation.Viruses · 2026Review
- Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.The Journal of allergy and clinical immunology · 2026Article
- The mycobiome, virome and archaeome in gastrointestinal cancers: molecular pathogenesis and therapeutic intervention.Molecular cancer · 2026Review
- The Gut-Pancreas Axis in Type 1 Diabetes: Emerging Insights into Microbiota and Immune Interactions.International journal of molecular sciences · 2026Review
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Development of the Gut Microbiota throughout the First Year of Life and Its Association with Socio-Emotional Development into Childhood.Developmental neuroscience · 2026Article
- Microbiome-mediated colonization resistance to and countermeasures of Klebsiella pneumoniae.Nature communications · 2026Article
- Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.Science advances · 2026Article
- Identify and characterize a carbapenem-resistant Salmonella enteritidis phage depolymerase Dpo52.Scientific reports · 2026Article
- Single cell viral tagging ofGut microbes · 2025Article
- The microbiome in cancer.iMeta · 2025Review
- A prevalent huge phage clade in human and animal gut microbiomes.bioRxiv : the preprint server for biology · 2025Article
- Unfolding the Mystery of Autoimmunity: The Environmental Determinants of Diabetes in the Young (TEDDY) Study.Diabetes care · 2025Review
- Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.bioRxiv : the preprint server for biology · 2025Article
- The gut virome in association with the bacteriome in gastrointestinal diseases and beyond: roles, mechanisms, and clinical applications.Precision clinical medicine · 2025Review
- Advancing RNA phage biology through meta-omics.Nucleic acids research · 2025Review
- Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy.Briefings in functional genomics · 2025Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.
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Registered trials
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