ArticleFrontiers in microbiology2020
Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics.
Article in Frontiers in microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Conditional superiorities and unaddressed bottlenecks: a critical review of artificial intelligence for waterborne microbial detection.Applied microbiology and biotechnology · 2026Review
- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
- Strategies for Actinobacteria Isolation, Cultivation, and Metabolite Production that Are Biologically Important.ACS omega · 2025Review
- How genomics can help unravel the evolution of endophytic fungi.World journal of microbiology & biotechnology · 2025Review
- Meta-omics assisted microbial gene and strain resources mining in contaminant environment.Engineering in life sciences · 2024Review
- Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome.mSphere · 2024Article
- Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq.Frontiers in microbiology · 2024Article
- scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.mSystems · 2023Article
- A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide.mSystems · 2023Review
- Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes.Microorganisms · 2023Article
- Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.International journal of molecular sciences · 2023Article
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner.Nucleic acids research · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Microbial Involvement in Carbon Transformation via CHBiology · 2021Article
- Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation.Frontiers in microbiology · 2021Article
- Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts.Frontiers in bioengineering and biotechnology · 2021Review
- Microbial single-cell omics: the crux of the matter.Applied microbiology and biotechnology · 2020Review
- Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors.Frontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.
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