ArticleNucleic acids research2023
MiMeDB: the Human Microbial Metabolome Database.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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
69 citing papers in PubMed, 101 citations in OpenAlex.
- Testosterone administration partially modulates gut microbiota responses to severe energy deficit.American journal of physiology. Endocrinology and metabolism · 2026Trial
- Article
- The role of gut microbiome in aging-associated diseases: where do we stand now and how technology will transform the future.Gut microbes · 2026Review
- Distinction of meal quality and interaction with the gut microbiota by breath volatilome analysis in humans.Gut microbes · 2026Article
- A geroprotective probiotic and its functional metabolite counteract inflammaging to extend healthspan.Nature aging · 2026Article
- SigMine and OPathDb: a literature-mining pipeline and database of potential opportunistic pathogens.Archives of microbiology · 2026Article
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Decoding Biothreats With FT-ICR-MS: Metabotyping of Bacillus cereus Spores Through Untargeted Metabolomics.Journal of mass spectrometry : JMS · 2026Article
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Mass spectrometry-based metabolomics approaches to interrogate host-microbiome interactions in mammalian systems.Natural product reports · 2026Review
- The microbiota-gut-brain axis: novel mechanisms and therapeutic frontiers in obesity and type 2 diabetes.NPJ biofilms and microbiomes · 2026Review
- Recent Trends in Metabolomics by NMR Spectroscopy.Angewandte Chemie (International ed. in English) · 2026Review
- Navigating multi-omic integration methods for human microbiome research.Nature microbiology · 2026Review
- Article
- RAW 264.7 macrophage cell line as a metabolomic model for analyzing and understanding inflammation processes.Naunyn-Schmiedeberg's archives of pharmacology · 2026Review
- An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut.Cell host & microbe · 2026Article
- Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.Analytical and bioanalytical chemistry · 2026Article
- Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data.bioRxiv : the preprint server for biology · 2026Article
- TidyMass2: advancing LC-MS untargeted metabolomics through metabolite origin inference and metabolic feature-based functional module analysis.Nature communications · 2026Article
- MiMeDB 2.0: the Human Microbial Metabolome Database for 2026.Nucleic acids research · 2026Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
Abstract
The Human Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, multi-omic, microbiome resource that connects: (i) microbes to microbial genomes; (ii) microbial genomes to microbial metabolites; (iii) microbial metabolites to the human exposome and (iv) all of these 'omes' to human health. MiMeDB was established to consolidate the growing body of data connecting the human microbiome and the chemicals it produces to both health and disease. MiMeDB contains detailed taxonomic, microbiological and body-site location data on most known human microbes (bacteria and fungi). This microbial data is linked to extensive genomic and proteomic sequence data that is closely coupled to colourful interactive chromosomal maps. The database also houses detailed information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that ultimately lead to the observed microbial metabolites in humans. Additional, extensively referenced data about the known or presumptive health effects, measured biosample concentrations and human protein targets for these compounds is provided. All of this information is housed in richly annotated, highly interactive, visually pleasing database that has been designed to be easy to search, easy to browse and easy to navigate. Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases. We believe that MiMeDB represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.
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What OpenQuestion holds
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.