ArticleNature protocols2014
Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes.
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 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
15 citing papers in PubMed.
- Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes.ISME communications · 2023Article
- Progress in the application of sustained-release drug microspheres in tissue engineering.Materials today. Bio · 2022Review
- Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion.Micromachines · 2022Article
- Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.Cell reports methods · 2022Article
- Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology.Trends in analytical chemistry : TRAC · 2021Review
- Meeting report of the fourth annual Tri-Service Microbiome Consortium symposium.Environmental microbiome · 2021Article
- High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.Journal of microbiology (Seoul, Korea) · 2020Article
- Panel 3: Genomics, precision medicine and targeted therapies.International journal of pediatric otorhinolaryngology · 2020Review
- Development of Anti-ImmunoTargets and therapy · 2020Article
- Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - A review.Journal of advanced research · 2019Review
- The trajectory of microbial single-cell sequencing.Nature methods · 2017Review
- Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.Genome announcements · 2015Article
- Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.PloS one · 2015Article
- Article
- Reconstructing each cell's genome within complex microbial communities-dream or reality?Frontiers in microbiology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assembling a complete genome from a single bacterial cell, termed single-cell genomics, is challenging with current technologies. Recovery rates of complete genomes from fragmented assemblies of single-cell templates significantly vary. Although increasing the amount of genomic template material by standard cultivation improves recovery, most bacteria are unfortunately not amenable to traditional cultivation, possibly owing to the lack of unidentified, yet necessary, growth signals and/or specific symbiotic influences. To overcome this limitation, we adopted and modified the method of cocultivation of single-captured bacterial cells in gel microdroplets (GMDs) to improve full genomic sequence recovery. By completing multiple genomes of two novel species derived from single cells, we demonstrated its efficacy on diverse bacterial species using human oral and gut microbiome samples. Here we describe a detailed protocol for capturing single bacterial cells, cocultivating them in medium and isolating microcolonies in GMDs with flow cytometry. Beginning with preliminary studies, obtaining GMDs with single microcolonies for whole-genome amplification may take ∼4 weeks.
Indexed as
Identifiers
24525754What OpenQuestion holds
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.