ArticlePeerJ2019
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Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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.
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Who cites it
24 citing papers in PubMed.
- Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety.Nature communications · 2023Trial
- Taxonomy bias in metagenome-assembled genome recovery.Microbial genomics · 2026Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Negativeome characterization and decontamination in early-life virome studies.Nature communications · 2025Article
- Diverse ssRNA viruses associated withmSphere · 2025Article
- Long oligos: direct chemical synthesis of genes with up to 1728 nucleotides.Chemical science · 2025Article
- De Novo Synthesis of Error-Free Long Oligos.Current protocols · 2024Article
- Nanopore and Illumina sequencing reveal different viral populations from human gut samples.Microbial genomics · 2024Article
- Viral potential to modulate microbial methane metabolism varies by habitat.Nature communications · 2024Article
- DeepCorr: a novel error correction method for 3GS long reads based on deep learning.PeerJ. Computer science · 2024Article
- A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil.Nature communications · 2023Article
- Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations.Microorganisms · 2022Article
- The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally.The ISME journal · 2022Article
- Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdomPeerJ · 2022Article
- Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.Microbiome · 2021Article
- Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome.Viruses · 2021Article
- Glacier ice archives nearly 15,000-year-old microbes and phages.Microbiome · 2021Article
- Article
- Stability of the human gut virome and effect of gluten-free diet.Cell reports · 2021Article
- Benchmarking microbial growth rate predictions from metagenomes.The ISME journal · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling
methodsHere we evaluate
resultsRead mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes.
conclusionsPCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved
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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.