SynthesisCell reports2023
MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.
Synthesis in Cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- A functional immune-based platform for donor-recipient matching in faecal microbiota transplantation for inflammatory bowel disease.EBioMedicine · 2026Article
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.bioRxiv : the preprint server for biology · 2026Article
- Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.Microbiology spectrum · 2026Article
- CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.Briefings in bioinformatics · 2026Article
- Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.Cell reports. Medicine · 2026Article
- Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.Microbiome · 2026Article
- Metabolic stress sensing by epithelial RXRα links westernization of diet with Crohn's disease.Cell metabolism · 2026Article
- Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.iScience · 2025Article
- Article
- Loss of sialic acid side-chainProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.mSystems · 2025Review
- Next-Generation Sequencing Techniques to Diagnose Culture-Negative Subacute Native Aortic Endocarditis.Emerging infectious diseases · 2025Article
- Accurate prediction of absolute prokaryotic abundance from DNA concentration.Cell reports methods · 2025Article
- Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo.bioRxiv : the preprint server for biology · 2025Article
- γBMGC: A Comprehensive and Accurate Database for Screening TMAO-Associated Cardiovascular Diseases.Microorganisms · 2025Article
Corrections and comments
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Authors and funding
24 authors.
Funding
Abstract
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
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