ArticleNature protocols2017
In situ cultivation of previously uncultivable microorganisms using the ichip.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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Who cites it
113 citing papers in PubMed.
- Illuminating Antarctic Microbial Dark Matter:Environment & health (Washington, D.C.) · 2026Article
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- A roadmap to create FAIR collections of microbial strains.Nature microbiology · 2026Review
- SubCom analysis: dissecting microbial community functions into taxon-specific contributions and interaction contexts.Microbiome · 2026Article
- Minimal Computational Framework for Systematic Identification of Antimicrobial Targets.bioRxiv : the preprint server for biology · 2026Article
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- Unlocking Microbial Dark Matter: A Comprehensive Review of Isolation Technologies from Traditional Culturing to Single-Cell Technologies.Microorganisms · 2026Review
- Ribosomal RNA operon copy number: A trait-informed framework to close the microbial cultivation gap.iMetaOmics · 2026Article
- Targeted isolation of HNature protocols · 2026Review
- Antimicrobial Resistance: The Answers.British journal of biomedical science · 2026Review
- The adaptation chip: repurposing the principles of the ichip for guiding in situ experimental evolution.ISME communications · 2026Article
- Study on disinfection using wet wipes and UV irradiation for areas prone to condensate accumulation in the Chinese Space Station.Frontiers in microbiology · 2026Article
- Omics Technologies-Driven Research and Applications of Synthetic Biology.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Article
- Tunable lysis of functionalized nanocultures for efficient microbial and nucleic acid recovery.Chemical engineering journal (Lausanne, Switzerland : 1996) · 2025Article
- An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products.Microbial genomics · 2025Article
- Strategies Used for the Discovery of New Microbial Metabolites with Antibiotic Activity.Molecules (Basel, Switzerland) · 2025Review
- Article
- Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.Microbiology (Reading, England) · 2025Article
53 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Most microbial species remain uncultivated, and modifying artificial nutrient media brings only an incremental increase in cultivability. We reasoned that an alternative way to cultivate species with unknown requirements is to use naturally occurring combinations of growth factors. To achieve this, we moved cultivation into the microbes' natural habitat by placing cells taken from varying environmental samples into diffusion chambers, which are then returned to nature for incubation. By miniaturizing the chambers and placing only one to several cells into each chamber, we can grow and isolate microorganisms in axenic culture in one step. We call this cultivation platform the 'isolation chip', or 'ichip'. This platform has been shown to increase microbial recovery from 5- to 300-fold, depending on the study. Furthermore, it provides access to a unique set of microbes that are inaccessible by standard cultivation. Here we provide a simple protocol for building and applying ichips for environmental cultivation of soil bacteria as an example; the protocol consists of (i) preparing the ichip; (ii) collecting an environmental sample; (iii) serially diluting cells and loading them into the ichip; (iv) returning the ichip to the environment for incubation; (v) retrieving the ichip and harvesting grown material; and (vi) domestication of the ichip-derived colonies for growth in the laboratory. The ichip's full assembly and deployment is a relatively simple procedure that, with experience, takes ∼2-3 h. After in situ incubation, retrieval of the ichip and processing of its contents will take ∼1-4 h, depending on which specific procedures are used.
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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.