ArticleMicrobiome2022
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- Bridging the gap:Gut microbes · 2026Review
- It takes a village: how plant-associated bacterial communities socialise to shape plant growth and health.Essays in biochemistry · 2026Review
- Potential plastic biodegradation in lakes worldwide.Innovation (Cambridge (Mass.)) · 2026Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.MicrobiologyOpen · 2026Article
- Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.Foods (Basel, Switzerland) · 2026Review
- Unlocking Microbial Dark Matter: A Comprehensive Review of Isolation Technologies from Traditional Culturing to Single-Cell Technologies.Microorganisms · 2026Review
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.Journal of microbiology and biotechnology · 2026Article
- Article
- Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.Scientific data · 2026Article
- Bacterial Siderophore Production in Metal-Rich Environments: Underexplored Sources of Siderophores and Insights into Bioremediation.Journal of natural products · 2026Review
- Harnessing bacterial power and omics technologies for sustainable plastic waste biodegradation.Biodegradation · 2026Review
- Sulfur Oxidation by New and Non-Canonical Bacteria in a Subsurface Flow Constructed Wetland Treating Domestic Wastewater.Microorganisms · 2026Article
- Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals.Molecular ecology · 2026Review
- Vitamin BMicrobial genomics · 2026Article
- Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.BMC genomics · 2026Article
- Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.Applied and environmental microbiology · 2026Article
- RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.Microbiome · 2026Article
- Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features.Microorganisms · 2026Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.
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