ArticleBriefings in bioinformatics2022
Critical assessment of pan-genomic analysis of metagenome-assembled genomes.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Article
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- Pan-genome insights into genetic diversity, evolutionary dynamics, and pathogenic traits of Staphylococcus agnetis.BMC genomics · 2026Article
- Insights into novel diagnostic assay development, antimicrobial resistance, and pathogenicity inApplied and environmental microbiology · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Shotgun metagenomic and phenotypic characterization of indigenous lactic acid bacteria from raw milk artisanal cheeses: metagenomic functional insight and starter culture traits.Frontiers in microbiology · 2026Article
- Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?Frontiers in microbiology · 2026Article
- Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.Environmental microbiology · 2026Article
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
- Tracking putativemSystems · 2025Article
- Pangenome Analysis ofMicroorganisms · 2025Article
- Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.Antibiotics (Basel, Switzerland) · 2025Review
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.Nature communications · 2025Article
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Seven quick tips for gene-focused computational pangenomic analysis.BioData mining · 2024Article
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.Genome biology · 2024Article
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2 authors.
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Abstract
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
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