ArticleMicrobiome2016
A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.
Article in Microbiome, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Seasonal patterns of viromes in urban aquatic environments of Manitoba.Applied and environmental microbiology · 2025Article
- 20 years of research on giant viruses.Npj viruses · 2025Review
- Evaluating Atlantic Salmon (Pathogens (Basel, Switzerland) · 2024Article
- Activated sludge prokaryote and eukaryote characterization in a pulp mill facility using amplicon sequencing.Heliyon · 2024Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- Review
- Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming.Microbial ecology · 2023Article
- Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.Frontiers in microbiology · 2023Article
- Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples.STAR protocols · 2022Article
- Diagnostic Methods of Common Intestinal Protozoa: Current and Future Immunological and Molecular Methods.Tropical medicine and infectious disease · 2022Review
- Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada.The Science of the total environment · 2022Article
- Microbes in the built environment.Scientific reports · 2022Article
- Production of microalgae with high lipid content and their potential as sources of nutraceuticals.Phytochemistry reviews : proceedings of the Phytochemical Society of Europe · 2022Review
- Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant.Environmental microbiome · 2022Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Article
- DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables.Microbial biotechnology · 2021Review
- High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.Nature methods · 2021Article
- Article
- Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
backgroundStudies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary.
resultsWe developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels.
conclusionThis study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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