ArticleNucleic acids research2016
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- The Landscape of Genetic Content in the Gut and Oral Human Microbiome.Cell host & microbe · 2019Pooled it
- Assessing the safety of microbiome perturbations.Microbial genomics · 2025Review
- Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.Frontiers in microbiology · 2025Review
- Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment.Briefings in bioinformatics · 2024Review
- The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.Database : the journal of biological databases and curation · 2024Article
- The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.Animal microbiome · 2023Article
- A display and analysis platform for gut microbiomes of minority people and phenotypic data in China.Scientific reports · 2023Article
- A display and analysis platform for gut microbiomes of minority people and phenotypic data in China.Scientific reports · 2023Article
- The gut mucin-microbiota interactions: a missing key to optimizing endurance performance.Frontiers in physiology · 2023Review
- CDEMI: Characterizing differences in microbial composition and function in microbiome data.Computational and structural biotechnology journal · 2023Article
- Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome.Nature communications · 2022Article
- AMDB: a database of animal gut microbial communities with manually curated metadata.Nucleic acids research · 2022Article
- Generating human papillomavirus (HPV) reference databases to maximize genomic mapping.Archives of virology · 2022Article
- Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases.Frontiers in immunology · 2022Review
- Intestinal Barrier in Human Health and Disease.International journal of environmental research and public health · 2021Review
- Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Discovering microbe-disease associations from the literature using a hierarchical long short-term memory network and an ensemble parser model.Scientific reports · 2021Article
- GIMICA: host genetic and immune factors shaping human microbiota.Nucleic acids research · 2021Article
- Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.MicrobiologyOpen · 2020Article
- Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.Microbiome · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease.
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Registered trials
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.