ArticlePeerJ2016
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
53 citing papers in PubMed, 101 citations in OpenAlex.
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- Using Carrier DNA in Ultra-Low Input Library Preparations for Next-Generation Sequencing.Journal of biomolecular techniques : JBT · 2026Article
- Whole genome sequencing of Cryptosporidium from low DNA inputs without whole genome amplification.Molecular biology reports · 2025Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
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- Ballistic Microscopy (BaM).bioRxiv : the preprint server for biology · 2025Article
- Genetic isolation and metabolic complexity of an Antarctic subglacial microbiome.Nature communications · 2025Article
- Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.Microbial genomics · 2025Article
- Metagenomic airborne resistome from urban hot spots through the One Health lens.Environmental microbiology reports · 2024Article
- A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.Nature communications · 2024Article
- Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China.Frontiers in microbiology · 2024Article
- Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP.Nature communications · 2023Article
- Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies.Antibiotics (Basel, Switzerland) · 2023Article
- Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.Astrobiology · 2023Article
- Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea.Animal microbiome · 2023Article
- Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.International journal of molecular sciences · 2023Article
- Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for NThe ISME journal · 2022Article
- Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods.BMC biology · 2022Article
- Historical contingencies and phage induction diversify bacterioplankton communities at the microscale.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
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Registered trials
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.