ArticleNature communications2023
The genomic landscape of reference genomes of cultivated human gut bacteria.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Article
- Structural Variants in the Human Genome Associated With Gut Microbiome and Blood Metabolic Traits With Potential Causal Links.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrated Genomics and Phenotypic Analysis ofMicroorganisms · 2026Article
- Lactobacillus gasseri TF08-1 Alleviates DSS-Induced Acute Colitis by Protecting Intestinal Epithelial Barrier.Probiotics and antimicrobial proteins · 2026Article
- Article
- Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.BMC microbiology · 2026Article
- Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.BMC microbiology · 2026Article
- Amelioration of colitis through restored gut ecology using Christensenella intestinihominis AF73-05CM02 as a probiotic in mice.Communications biology · 2026Article
- Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.Cell genomics · 2026Article
- Case report ofASM case reports · 2026Article
- The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Mechanisms of constipation alleviation by Lacticaseibacillus paracasei BGI-N2: insights from genes to phenotypes.BMC microbiology · 2026Article
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms.Nucleic acids research · 2026Article
- Lacticaseibacillus rhamnosus OF44 with Potent Antimicrobial Activity: Evidence from the Complete Genome and Phenotypic Analysis.Probiotics and antimicrobial proteins · 2026Article
- Gut microbiota and gut-kidney axis in kidney diseases: therapeutic potential and perspectives of natural products.Frontiers in pharmacology · 2026Review
- Article
- Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.Genome medicine · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
- Cultivation and sequencing of microbiota members unveil the functional potential of yak gut microbiota.mSystems · 2025Article
- Smart Microbiomes: How AI Is Revolutionizing Personalized Medicine.Bioengineering (Basel, Switzerland) · 2025Review
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.
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