ArticleGenome research2013
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Cell-in-Bead-in-Droplet Platform for pH-Based Microfluidic Screening of Ureolytic Bacteria.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.The ISME journal · 2024Article
- A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.Genome biology · 2022Article
- Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology.Trends in analytical chemistry : TRAC · 2021Review
- Metagenomics: a path to understanding the gut microbiome.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Review
- Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.Nature protocols · 2021Article
- Strain-level epidemiology of microbial communities and the human microbiome.Genome medicine · 2020Review
- Host-Microbiome Interactions in the Era of Single-Cell Biology.Frontiers in cellular and infection microbiology · 2020Review
- Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria.The ISME journal · 2018Article
- The trajectory of microbial single-cell sequencing.Nature methods · 2017Review
- Dissecting the human microbiome with single-cell genomics.Genome medicine · 2017Review
- The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures.Scientific reports · 2017Article
- High-throughput automated microfluidic sample preparation for accurate microbial genomics.Nature communications · 2017Article
- MetaSort untangles metagenome assembly by reducing microbial community complexity.Nature communications · 2017Article
- Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung.Nature communications · 2017Article
- Single-cell genome sequencing: current state of the science.Nature reviews. Genetics · 2016Review
- Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples.PloS one · 2016Article
- Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.Genome announcements · 2015Article
- Article
- Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.PloS one · 2015Article
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21 authors.
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Abstract
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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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.