ArticleMicrobiome2020
A pipeline for targeted metagenomics of environmental bacteria.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 52 citations in OpenAlex.
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Environmental diversity ofmSystems · 2025Article
- Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds.PloS one · 2025Article
- Microbial single-cell applications under anoxic conditions.Applied and environmental microbiology · 2024Review
- SecMet-FISH: labeling, visualization, and enumeration of secondary metabolite producing microorganisms.FEMS microbiology ecology · 2024Article
- Unraveling metagenomics through long-read sequencing: a comprehensive review.Journal of translational medicine · 2024Review
- A targeted approach to enrich host-associated bacteria for metagenomic sequencing.FEMS microbes · 2024Article
- Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.Marine drugs · 2023Article
- Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.Microorganisms · 2023Article
- ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization.Frontiers in genetics · 2023Article
- Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.Frontiers in microbiology · 2023Review
- Ecosystem-specific microbiota and microbiome databases in the era of big data.Environmental microbiome · 2022Review
- Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes.ISME communications · 2022Article
- Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.Cell reports methods · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria.ISME communications · 2021Article
- Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review.Foods (Basel, Switzerland) · 2021Review
- Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments.Marine life science & technology · 2021Article
- Evaluation of RNAMicrobiology spectrum · 2021Article
- Visualization of Gene Reciprocity among Lactic Acid Bacteria in Yogurt by RNase H-Assisted Rolling Circle Amplification-FluorescenceMicroorganisms · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses.
methodsCells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity.
resultsPure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade.
conclusionsWith the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades. Video abstract.
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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.