ArticlePeerJ2020
Biases in genome reconstruction from metagenomic data.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Article
- Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.Animal microbiome · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- Article
- Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?Frontiers in microbiology · 2026Article
- Leveraging strain competition to address antimicrobial resistance with microbiota therapies.Gut microbes · 2025Review
- High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral,mSystems · 2025Article
- Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.MethodsX · 2025Article
- Nanopore Sequencing of Amoebophrya Species Reveals Novel Collection of Bacteria Putatively Associated With Karlodinium veneficum.Genome biology and evolution · 2025Article
- A metagenomic perspective on the microbial prokaryotic genome census.Science advances · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- Article
- From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.Microbiome · 2024Article
- Article
- Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study.Frontiers in microbiology · 2024Article
- The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.Frontiers in microbiology · 2024Article
- CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning.Nature methods · 2023Article
- Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach.Frontiers in microbiology · 2023Review
- Metaphor-A workflow for streamlined assembly and binning of metagenomes.GigaScience · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAdvances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs.
methodsWe compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the
resultsRepeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
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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.