ArticleMicrobiome2021
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 111 papers, 1 of them a synthesis that pooled it.
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Who cites it
111 citing papers in PubMed, 1 synthesis or guideline pooled it, 188 citations in OpenAlex.
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- From Multi-Omics to Molecular Causality: A Five-Tier Evidence Framework for the Single-Bacterium-Metabolite Axis in IBD.Microorganisms · 2026Review
- Gut microbial culturomics identifies autism-associatedMicrobiology spectrum · 2026Article
- Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.JHEP reports : innovation in hepatology · 2026Article
- The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.Journal of natural medicines · 2026Review
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- NovelGut · 2026Article
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- The butyrate-producing Gram-positive human gut bacterium, Hoskinsella mucinilytica, selectively targets host mucin N-acetylhexosamines.The Journal of biological chemistry · 2026Article
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- Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.Current microbiology · 2026Article
- Immunomodulatory Role of Milk on Gut Microbiota: Implications for Enhancing Oral Vaccine Efficacy.Probiotics and antimicrobial proteins · 2026Review
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- Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.Folia microbiologica · 2026Article
51 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
19 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn gut microbiome studies, the cultured gut microbial resource plays essential roles, such as helping to unravel gut microbial functions and host-microbe interactions. Although several major studies have been performed to elucidate the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species have not been cultured to date. Large-scale gut microbial isolation and identification as well as availability to the public are imperative for gut microbial studies and further characterizing human gut microbial functions.
resultsIn this study, we constructed a human Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn ) through the cultivation of 10,558 isolates from 31 sample mixtures of 239 fresh fecal samples from healthy Chinese volunteers, and deposited 1170 strains representing 400 different species in culture collections of the International Depository Authority for long-term preservation and public access worldwide. Following the rules of the International Code of Nomenclature of Prokaryotes, 102 new species were characterized and denominated, while 28 new genera and 3 new families were proposed. hGMB represented over 80% of the common and dominant human gut microbial genera and species characterized from global human gut 16S rRNA gene amplicon data (n = 11,647) and cultured 24 "most-wanted" and "medium priority" taxa proposed by the Human Microbiome Project. We in total sequenced 115 genomes representing 102 novel taxa and 13 previously known species. Further in silico analysis revealed that the newly sequenced hGMB genomes represented 22 previously uncultured species in the Unified Human Gastrointestinal Genome (UHGG) and contributed 24 representatives of potentially "dark taxa" that had not been discovered by UHGG. The nonredundant gene catalogs generated from the hGMB genomes covered over 50% of the functionally known genes (KEGG orthologs) in the largest global human gut gene catalogs and approximately 10% of the "most wanted" functionally unknown proteins in the FUnkFams database.
conclusionsA publicly accessible human Gut Microbial Biobank (hGMB) was established that contained 1170 strains and represents 400 human gut microbial species. hGMB expands the gut microbial resources and genomic repository by adding 102 novel species, 28 new genera, 3 new families, and 115 new genomes of human gut microbes. Video abstract.
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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.