ArticleNature communications2015
Harnessing the landscape of microbial culture media to predict new organism-media pairings.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis 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.
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.
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Who cites it
75 citing papers in PubMed, 1 synthesis or guideline pooled it, 161 citations in OpenAlex.
- A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities.Applied and environmental microbiology · 2022Pooled it
- Bridging the gap:Gut microbes · 2026Review
- Machine learning-based linking of bacterial genomes to optimal growth pH: a foundation for rational microbial engineering.Journal of animal science and biotechnology · 2026Article
- Cleaning reshapes bacterial communities in public toilets through disturbance and random reassembly.Scientific reports · 2026Article
- Harnessing the Gut Microbes of Low Abundance With a Bent-Capillary-Centrifugal-Driven (BCCD) Microdroplet Method.MicrobiologyOpen · 2026Article
- Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.Microbiology (Reading, England) · 2025Article
- Nitrogen cycle induced by plant growth-promoting rhizobacteria drives "microbial partners" to enhance cadmium phytoremediation.Microbiome · 2025Article
- Metagenomic and Physicochemical Analyses Reveal Microbial Community and Functional Differences Between Three Different Grades of Hongxin Low-Temperature Daqu.Foods (Basel, Switzerland) · 2025Article
- The Gut Bacteria ofInsects · 2025Article
- Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.The ISME journal · 2025Article
- Explainable rule-based prediction of cultivation media for microbes.Computational and structural biotechnology journal · 2025Article
- Article
- Plant-microbe interactions: PGPM as microbial inoculants/biofertilizers for sustaining crop productivity and soil fertility.Current research in microbial sciences · 2025Review
- Unveiling Diversity and Function: Venom-Associated Microbes in Two Spiders, Heteropoda venatoria and Chilobrachys guangxiensis.Microbial ecology · 2024Article
- Review
- Agricultural Pest Management: The Role of Microorganisms in Biopesticides and Soil Bioremediation.Plants (Basel, Switzerland) · 2024Review
- The Role and Mechanism of Probiotics Supplementation in Blood Glucose Regulation: A Review.Foods (Basel, Switzerland) · 2024Review
- Updated roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence.Zoological research · 2024Review
- Advances in the isolation, cultivation, and identification of gut microbes.Military Medical Research · 2024Review
- Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.Microbial ecology · 2024Article
15 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
7 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism-media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts.
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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.