ArticleISME communications2022
Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater.
Article in ISME communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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.
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Who cites it
27 citing papers in PubMed, 47 citations in OpenAlex.
- Single-organelle DNA-sequencing of chloroplasts and mitochondria in Arabidopsis thaliana.BMC plant biology · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- Risk assessment of plant-to-bacterium transgene flow associated with novel small synthetic genome (minisynplastome) platforms for plastid genetic engineering.FEMS microbiology ecology · 2026Article
- Single-cell Genomic Analysis of Fiber-adhering Rumen Bacteria during an in situ Incubation of Timothy Hay.Microbes and environments · 2026Article
- Single-cell genomic profiling of antimicrobial resistance inFrontiers in microbiology · 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
- Single-cell genome analysis of a feminizingMicrobial genomics · 2025Article
- Integrating serotyping, MLST, and phenotypic data: decoding the evolutionary drivers ofApplied and environmental microbiology · 2025Article
- From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance.Molecular biology and evolution · 2025Article
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.Innovation (Cambridge (Mass.)) · 2025Article
- From specialization to broad adoption: Key trends in droplet microfluidic innovations enhancing accessibility to non-experts.Biomicrofluidics · 2025Article
- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
- Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.Frontiers in microbiology · 2025Article
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.Microbiome · 2024Article
- Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.Scientific data · 2024Article
- Uncovering Endolysins against Methicillin-ResistantACS infectious diseases · 2024Article
- Targeted whole-genome recovery of single viral species in a complex environmental sample.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.Biophysical reviews · 2024Review
- Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere.mSphere · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
Identifiers
What 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.