ArticleMicrobiome2014
Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.
Article in Microbiome, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
67 citing papers in PubMed.
- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
- The human skin virome: Ecological dynamics, aberrant profiles, and therapeutic opportunities.Cell host & microbe · 2026Review
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.bioRxiv : the preprint server for biology · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Decoding microbiome responses to quarantine potato wart disease: first insights into suppression and biocontrol by full-length 16S rRNA gene profiling and functional prediction.Frontiers in plant science · 2025Article
- Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments.Microbiome · 2024Article
- Nanopore and Illumina sequencing reveal different viral populations from human gut samples.Microbial genomics · 2024Article
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome.mSphere · 2024Article
- The Diversity of Bacteriophages in the Human Gut.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Soil viral diversity, ecology and climate change.Nature reviews. Microbiology · 2023Review
- Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.Marine drugs · 2023Article
- Interpersonal variability of the human gut virome confounds disease signal detection in IBD.Communications biology · 2023Article
- Long-Read Metagenomics and CAZyme Discovery.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Characterization of the human gut virome in metabolic and autoimmune diseases.Inflammation and regeneration · 2022Review
- How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner.Nucleic acids research · 2022Article
- Article
- Record-Breaking Rain Event Altered Estuarine Viral Assemblages.Microorganisms · 2022Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
backgroundShotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested.
resultsUsing mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes.
conclusionsMDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.
Identifiers
What OpenQuestion holds
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.