ArticleNAR genomics and bioinformatics2022
mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The human gut microbeApplied and environmental microbiology · 2026Article
- Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.Nature communications · 2026Article
- Uncovering the Prokaryotic Diversity of Hypersaline Soils of Odiel Saltmarshes Natural Area Through Metagenome-Assembled Genomes.Microorganisms · 2026Article
- Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome.Environmental microbiome · 2026Article
- Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.Nature communications · 2025Article
- Microbial model communities exhibit widespread metabolic interdependencies.Communications biology · 2025Article
- Comprehensive analysis ofGut microbes · 2025Article
- Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.Nature communications · 2025Article
- Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.Scientific reports · 2025Article
- Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.Animal microbiome · 2025Article
- Phenotypic and genomic analysis of the emerging poultry pathogenMicrobial genomics · 2025Article
- The effect ofMicrobiology spectrum · 2024Article
- Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.Nature microbiology · 2024Article
- Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms.Scientific data · 2024Article
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater.The ISME journal · 2024Article
- Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.ISME communications · 2024Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Linking prokaryotic genome size variation to metabolic potential and environment.ISME communications · 2023Article
- Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.Environmental microbiology · 2022Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.
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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.