ArticleNature biotechnology2019
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 316 papers, 2 of them syntheses that pooled it.
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316 citing papers in PubMed, 2 syntheses or guidelines pooled it, 593 citations in OpenAlex.
- Maast: genotyping thousands of microbial strains efficiently.Genome biology · 2023Pooled it
- A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.Microbiome · 2021Pooled it
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- Decoding strain level interactions betweenVirulence · 2026Article
- gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota.Journal of molecular biology · 2026Article
- Gut Microbiota as a Molecular Regulator of Mineral Homeostasis in Horses: Mechanisms and Future Perspectives.International journal of molecular sciences · 2026Review
- MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.Nature microbiology · 2026Article
- Polysaccharides PFP1-1 Activate Root "Recruitment Signals": Beneficial Bacteria-Mediated Rhizoctonia Resistance in Cotton.Plant, cell & environment · 2026Article
- Protective Effect of Apiaceous Vegetables against Total Western Diet- and Dextran Sulfate Sodium-Induced Colitis in Mice.The Journal of nutrition · 2026Article
- Gut microbial culturomics identifies autism-associatedMicrobiology spectrum · 2026Article
- Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.Nature genetics · 2026Article
- Lactobacillus gasseri TF08-1 Alleviates DSS-Induced Acute Colitis by Protecting Intestinal Epithelial Barrier.Probiotics and antimicrobial proteins · 2026Article
- A microbial consortium constructed with gut microbes of Chinese native chicken breeds protects chicks against Salmonella infection.Journal of animal science and biotechnology · 2026Article
- Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.bioRxiv : the preprint server for biology · 2026Article
- Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra.Nature communications · 2026Article
- Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.mSystems · 2026Review
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- The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
256 more citing papers are in PubMed but not listed here.
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Authors and funding
31 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.