ArticleScientific reports2018
Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 62 citations in OpenAlex.
- CoSAG-nf: a scalable nextflow pipeline for co-assembly, optimization, and interactive visualization of high-throughput single-cell genomes.Bioinformatics (Oxford, England) · 2026Article
- Single-cell Genomic Analysis of Fiber-adhering Rumen Bacteria during an in situ Incubation of Timothy Hay.Microbes and environments · 2026Article
- 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
- Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.BMC cancer · 2025Article
- High-throughput single-cell sequencing of activated sludge microbiome.Environmental science and ecotechnology · 2025Article
- Insights into human respiratory microbiome under dysbiosis and its analysis tool.Frontiers in microbiomes · 2025Review
- Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.Biophysical reviews · 2024Review
- - Invited Review - The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production.Animal bioscience · 2024Article
- Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere.mSphere · 2024Article
- Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage.Journal of advanced research · 2023Review
- A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters.Scientific data · 2023Article
- Revealing within-species diversity in uncultured human gut bacteria with single-cell long-read sequencing.Frontiers in microbiology · 2023Article
- Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.Computational and structural biotechnology journal · 2023Review
- Chimera: The spoiler in multiple displacement amplification.Computational and structural biotechnology journal · 2023Review
- Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral.Microbiome · 2022Article
- Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater.ISME communications · 2022Article
- How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner.Nucleic acids research · 2022Article
- Strain-level profiling of viable microbial community by selective single-cell genome sequencing.Scientific reports · 2022Article
- Single-cell metabolite detection and genomics reveals uncultivated talented producer.PNAS nexus · 2022Article
- Why sequence all eukaryotes?Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences. Here, we describe Cleaning and Co-assembly of a Single-Cell Amplified Genome (ccSAG), a novel analytical workflow to obtain composite single-cell genomes with elimination of sequence errors. By the integration of ccSAG with a massively parallel single-cell genome amplification platform based on droplet microfluidics, we can generate multiple SAGs and effectively integrate them into the composite genomes quality equivalent to the data obtained from bulk DNA. We obtained two novel draft genomes from single gut microbial cells with high completeness (>96.6%) and extremely low contamination (<1.25%). Moreover, we revealed the presence of single nucleotide polymorphisms in the specific gene by sequence comparison at the single-cell level. Thus, the workflow yields near-complete genomes from uncultured microbes, and enables analyses of genetic heterogeneity within identical strains.
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