ArticleNature biotechnology2023
High-throughput microbial culturomics using automation and machine learning.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
126 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Microbiota-Focused Dietary Approaches to Support Health: A Systematic Review.The Journal of nutrition · 2025Pooled it
- Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.Gut microbes · 2026Review
- Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition.Gut microbes · 2026Review
- Bridging the gap:Gut microbes · 2026Review
- The "oral-gut axis" transmission of microorganisms in colorectal cancer: Insights fromVirulence · 2026Review
- Accelerating natural product discovery, characterization and engineering by biofoundries.Natural product reports · 2026Review
- Insights into Microbiota-Vaccine Crosstalk in Humans: Mechanisms, Modulators, and Translational Horizons.Vaccines · 2026Review
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- Microbial Signals in Cancer: Dissecting Host-Microbiota-Tumor Interactions and Potential Therapeutic Strategy.MedComm · 2026Review
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Article
- Review
- Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.Nature reviews. Microbiology · 2026Review
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Article
- Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra.Nature communications · 2026Article
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Microbial biobanking: safeguarding the tiny treasures for sustainable human welfare.Folia microbiologica · 2026Review
- Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.mSystems · 2026Review
- Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.Foods (Basel, Switzerland) · 2026Review
66 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.
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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.