Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.
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| Main Authors: | , , , , , |
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| Format: | Artículo científico |
| Language: | en |
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NAR genomics and bioinformatics
2026
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| _version_ | 1868266056173223936 |
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| author | Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J |
| author_facet | Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J |
| collection | PubMed - marine biology |
| contents | Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring. Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J Animals Rivers Biodiversity Metagenomics Environmental Monitoring Humans Nanopore Sequencing DNA, Environmental Environmental Health Animals, Wild Metagenome As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, ) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them. |
| format | Artículo científico |
| id | pubmed_42038409 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | NAR genomics and bioinformatics |
| record_format | pubmed |
| spellingShingle | Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring. Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J Animals Rivers Biodiversity Metagenomics Environmental Monitoring Humans Nanopore Sequencing DNA, Environmental Environmental Health Animals, Wild Metagenome Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring. Nousias, Orestis Duffy, Fiona G Duffy, Isabelle J McCauley, Mark Whilde, Jenny Duffy, David J Animals Rivers Biodiversity Metagenomics Environmental Monitoring Humans Nanopore Sequencing DNA, Environmental Environmental Health Animals, Wild Metagenome As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, ) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them. |
| title | Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring. |
| topic | Animals Rivers Biodiversity Metagenomics Environmental Monitoring Humans Nanopore Sequencing DNA, Environmental Environmental Health Animals, Wild Metagenome |
| url | https://pubmed.ncbi.nlm.nih.gov/42038409/ |