ArticleNature protocols2014
Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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Who cites it
158 citing papers in PubMed, 301 citations in OpenAlex.
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- Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.Nature microbiology · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.bioRxiv : the preprint server for biology · 2025Article
- Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening.Molecular ecology resources · 2025Article
- Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.Innovation (Cambridge (Mass.)) · 2025Article
- Ultra-sensitive fluorescence-activated droplet single-cell sorting based on Tetramer-HCR-EvaGreen amplification.Microsystems & nanoengineering · 2025Article
- Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities.The ISME journal · 2025Article
98 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell genomics is a powerful tool for exploring the genetic makeup of environmental microorganisms, the vast majority of which are difficult, if not impossible, to cultivate with current approaches. Here we present a comprehensive protocol for obtaining genomes from uncultivated environmental microbes via high-throughput single-cell isolation by FACS. The protocol encompasses the preservation and pretreatment of differing environmental samples, followed by the physical separation, lysis, whole-genome amplification and 16S rRNA-based identification of individual bacterial and archaeal cells. The described procedure can be performed with standard molecular biology equipment and a FACS machine. It takes <12 h of bench time over a 4-d time period, and it generates up to 1 μg of genomic DNA from an individual microbial cell, which is suitable for downstream applications such as PCR amplification and shotgun sequencing. The completeness of the recovered genomes varies, with an average of ∼50%.
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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.