ArticleNature communications2019
An in vitro model maintaining taxon-specific functional activities of the gut microbiome.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 2 of them syntheses that pooled it.
What it found
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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.
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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
93 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Recent Developments and Applicability of In Vitro Gut Microbiota Models in Biomedical Research and Digestive Diseases-A Systematic Review.Medicina (Kaunas, Lithuania) · 2026Pooled it
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium.NPJ biofilms and microbiomes · 2022Pooled it
- Microbes and medicines: interrelationships between pharmaceuticals and the gut microbiome.Gut microbes · 2026Review
- Tissue-specific microbiota dictates the competitive dynamics ofThe veterinary quarterly · 2026Article
- Establishment of anmSystems · 2026Article
- Transferable genetic toolsets for nonmodel gut Clostridia enable in vivo reversible control of metabolite production.Nature biotechnology · 2026Article
- A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.Journal of bacteriology · 2026Article
- Protocol for preparing fiber-defined simulated media for growth profiling of diverse human gut bacterial isolates.STAR protocols · 2026Article
- Metabolomic Characterization of Baby Spinach Phenolics Transformation During Gastrointestinal Digestion and Microbiome-Mediated Metabolism.Foods (Basel, Switzerland) · 2026Article
- Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes.NPJ biofilms and microbiomes · 2026Article
- Microbiota utilization of intestinal amino acids modulates cancer progression and anticancer immunity.Cell host & microbe · 2026Article
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
- Article
- Carbohydrate competition by Enterobacteriaceae enhances colonization resistance to carbapenem-resistant hypervirulent K. pneumoniae.Microbiome · 2025Article
- Precision Antimicrobial Therapy Against Fusobacterium nucleatum Using Bioengineered Probiotics Expressing Guided Antimicrobial Peptides (gAMPs).Microbial biotechnology · 2025Article
- Optimized Protocol for the Collection, Cryopreservation, and In Vitro Cultivation of Human Gut Microbiota for Toxicomicrobiomics Applications.Bio-protocol · 2025Article
- Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.Nature communications · 2025Article
- Cystic fibrosis and inflammatory bowel disease: parallels in gut physiology and microbiota.Journal of bacteriology · 2025Review
- A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.bioRxiv : the preprint server for biology · 2025Article
- Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome.NPJ biofilms and microbiomes · 2025Article
33 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
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vitro gut microbiome models could provide timely and cost-efficient solutions to study microbiome responses to drugs. For this purpose, in vitro models that maintain the functional and compositional profiles of in vivo gut microbiomes would be extremely valuable. Here, we present a 96-deep well plate-based culturing model (MiPro) that maintains the functional and compositional profiles of individual gut microbiomes, as assessed by metaproteomics, while allowing a four-fold increase in viable bacteria counts. Comparison of taxon-specific functions between pre- and post-culture microbiomes shows a Pearson's correlation coefficient r of 0.83 ± 0.03. In addition, we show a high degree of correlation between gut microbiome responses to metformin in the MiPro model and those in mice fed a high-fat diet. We propose MiPro as an in vitro gut microbiome model for scalable investigation of drug-microbiome interactions such as during high-throughput drug screening.
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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.