ArticleNature biotechnology2019
A human gut bacterial genome and culture collection for improved metagenomic 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 311 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
311 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.Microbial ecology · 2024Pooled it
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- [Progress in the relationship between head and neck squamous cell carcinom and the microbial community].Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery · 2023Pooled it
- Review
- Endocannabinoids and related lipids in host metabolism-gut microbiome signalling.Nature reviews. Endocrinology · 2026Review
- Designing fiber-gut microbiome interactions with active learning.Nature chemical biology · 2026Article
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 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
- Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra.Nature communications · 2026Article
- Metabolism of β-mannans by representative, understudied Bacillota species from the human colon.FEMS microbiology ecology · 2026Article
- Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.mSystems · 2026Review
- Article
- Antagonism by the type VI secretion system ofProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploring the predominant factors associated with shaping the cultivable swine gut microbiota of Wuzhishan piglets under in vitro cultivation conditions.BMC microbiology · 2026Article
- Tongue-coating microbiome as a predictor of solid tumors: an updated scoping review of clinical studies.Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan · 2026Article
- Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.Microbiome · 2026Article
- Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.Nature communications · 2026Article
- Distribution and activity of nitrate and nitrite reductases in the microbiota of the human intestinal tract.The FEBS journal · 2026Article
- Article
251 more citing papers are in PubMed but not listed here.
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17 authors.
Funding
Abstract
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.
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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.