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Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.

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Název: Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.
Autoři: Verhoeven, Joost Theo Petra1 (AUTHOR), Malwe, Aditya Sanjay1 (AUTHOR), Roussel, Nathan2 (AUTHOR), Nielsen, Ida Broman1 (AUTHOR), Mak, Sarah S. T.1 (AUTHOR), Nielsen, Tue Kjærgaard3 (AUTHOR), Barnes, Christopher James1,2 (AUTHOR) drcjbarnes@gmail.com
Zdroj: New Phytologist. Nov2025, Vol. 248 Issue 4, p1620-1624. 5p.
Témata: *ADAPTIVE sampling (Statistics), *METAGENOMICS, *COLLECTION & preservation of biological specimens, *MICROBIAL communities, *CORN, *MICROBIAL ecology, *NANOPORES, *NUCLEOTIDE sequencing
Abstrakt: The article focuses on the use of adaptive sampling and adaptive depletion techniques in metagenomic studies to enhance the efficiency of profiling microbial communities in maize plants, particularly when host DNA predominates. Researchers utilized Oxford Nanopore Technologies' sequencing capabilities to demonstrate that adaptive depletion can significantly increase the proportion of microbial reads from maize roots and rhizosphere soil, achieving notable improvements in microbial read representation without additional laboratory complexity. The study highlights the potential of this method to facilitate more effective microbial ecology research, especially in scenarios where a reference host genome is available. However, it also notes limitations, such as the requirement for a reference genome and the higher error rates associated with nanopore sequencing compared to other platforms. [Extracted from the article]
Databáze: Academic Search Index
Popis
Abstrakt:The article focuses on the use of adaptive sampling and adaptive depletion techniques in metagenomic studies to enhance the efficiency of profiling microbial communities in maize plants, particularly when host DNA predominates. Researchers utilized Oxford Nanopore Technologies' sequencing capabilities to demonstrate that adaptive depletion can significantly increase the proportion of microbial reads from maize roots and rhizosphere soil, achieving notable improvements in microbial read representation without additional laboratory complexity. The study highlights the potential of this method to facilitate more effective microbial ecology research, especially in scenarios where a reference host genome is available. However, it also notes limitations, such as the requirement for a reference genome and the higher error rates associated with nanopore sequencing compared to other platforms. [Extracted from the article]
ISSN:0028646X
DOI:10.1111/nph.70450