ArticleMicrobes and environments2017
Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.
Article in Microbes and environments, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.Microbial genomics · 2025Article
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- Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.Nature communications · 2024Article
- Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.The ISME journal · 2024Article
- Accelerated Iron Corrosion by Microbial Consortia Enriched from Slime-like Precipitates from a Corroded Metal Apparatus Deployed in a Deep-sea Hydrothermal System.Microbes and environments · 2024Article
- Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations.Viruses · 2023Article
- Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions.mSphere · 2023Article
- First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.Frontiers in microbiology · 2023Article
- Bullet-shaped magnetosomes and metagenomic-based magnetosome gene profiles in a deep-sea hydrothermal vent chimney.Frontiers in microbiology · 2023Article
- Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods.BMC biology · 2022Article
- FourMicrobiology resource announcements · 2022Article
- Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.Nature microbiology · 2022Article
- Symbiont Community Composition inApplied and environmental microbiology · 2022Article
- Diverse DNA modification in marine prokaryotic and viral communities.Nucleic acids research · 2022Article
- Multispecies Populations of MethanotrophicApplied and environmental microbiology · 2022Article
- Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures.Microbes and environments · 2022Article
- Microbiologically influenced corrosion of stainless steel independent of sulfate-reducing bacteria.Frontiers in microbiology · 2022Article
- One-YearApplied and environmental microbiology · 2021Article
- Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments.The ISME journal · 2020Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.
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