CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

2023/07/27 by Alex Chklovski, Donovan H. Parks, Ben J. Woodcroft +1 · 113 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Gut microbiota and health #Microbial Community Ecology and Physiology

paper · doi:10.1038/s41592-023-01940-w

crossref issued 2023/07/27 · crossref published 2023/07/27 · crossref published-online 2023/07/27 · openalex publication_date 2023/07/27 · crossref created 2023/07/27 · crossref published-print 2023/08/01 · crossref deposited 2024/03/22 · openalex created_date 2025/10/10 · crossref indexed 2026/07/30 · openalex updated_date 2026/07/31

Citations

• Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
• DRAM for distilling microbial metabolism to automate the curation of microbiome function

Cited by

• Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity
• Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation
• Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US
• Magnetotactic Bdellovibrionota from a ferruginous spring
• A comprehensive genome-centred taxonomy for agrobacteria and rhizobia in the Bartonellaceae and Rhizobiaceae families
• Caldiplasma sukawensis gen. nov., sp. nov., and Cuniculiplasma thermophilum sp. nov., mesophilic, acidophilic, cell–wall–less, archaea of the order Thermoplasmatales, isolated from extremely acidic hot spring
• Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau
• Evolutionary analysis of transcription elongation factors reveals conserved and lineage-specific regulatory domains
• Robust ammonia oxidation by “ Candidatus Nitrosacidococcus tergens” across a broad pH range
• Ten novel psychrophilic Flavobacterium species from Tibetan Plateau glaciers define a cryospheric lineage with global cold-origin relatives
• Genome‐based polyphasic taxonomy of desert‐derived Kineococcus reveals nine novel species with plant growth‐promoting traits
• Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts
• Ecological plasticity of Halanaerobium microorganisms across terrestrial saline to hypersaline subsurface environments
• Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates
• Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly
• Methanotrophic flexibility of ‘ Ca . Methanoperedens’ and its interactions with sulfate-reducing bacteria in the sediment of meromictic Lake Cadagno
• Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?
• Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots
• Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers
• A molecular inventory of the faecal microbiomes of 23 marsupial species
• Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin
• Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities
• Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI
• Evolutionary Flexibility of Ribosome Biogenesis in Bacteria
• Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling
• Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities
• Mucilaginibacter aureus sp. nov. and Mucilaginibacter sediminis sp. nov., isolated from wetland soil
• The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With ‘ Candidatus Mirabilia Symbiotica’
• A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
• Pseudogenization of the chaperonin system in ‘Candidatus Phytoplasma pruni’ revealed by genome sequencing and comparative genomics
• Metabolic capacities of large “pillotinaceous” spirochetes from termite guts and their placement among Breznakiellaceae
• Genomic and phenotypic characterization of a human gut Methanobrevibacter intestini strain G0370_i3 isolated in Gabon
• Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota
• Flagellimonas ulvae sp. nov. and Flagellimonas rhodophyticola sp. nov., isolated from marine algae
• Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition
• Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota
• Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura
• Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data
• Gut Pathobiont–Derived Outer Membrane Vesicles Drive Liver Inflammation and Fibrosis in Primary Sclerosing Cholangitis–Associated Inflammatory Bowel Disease
• Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications
• The plasmid-borne hipBA operon of Klebsiella michiganensis encodes a potent plasmid stabilization system
• Core Microbiota Drives Host-Specific Growth Enhancement: Evidence in a Harmful Algal Bloom Causing Dinoflagellate Prorocentrum lima
• Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing
• Promicromonospora noduliphila sp. nov., a nodulation-enhancing actinobacterium isolated from the root nodules of grey-hair acacia planted in the Khurais desert, Saudi Arabia
• From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments
• Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes
• Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database
• Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges
• Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam
• Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler
• Investigating the role of bacterial raw milk community members in chlorate reduction
• Genomic analysis of the widely distributed Acidobacteriota members reveals their overlooked metabolic roles
• Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments
• Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia
• Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams
• Environmental surveillance of bacteria in a new intensive care unit using plate sweeps
• Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
• Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes
• Ecosystem retrogression enhances cross‐domain microbial stability and increases the genetic potential for nutrient cycling
• Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges
• Discovery and genomics of H2-oxidizing/O2-reducing Deferribacterota ectosymbiotic with protists in the guts of termites and a Cryptocercus cockroach
• Pseudomonas lyxosi sp. nov., Pseudomonas arabinosi sp. nov. and Pseudomonas frigoris sp. nov., isolated from glaciers
• Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper
• CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset
• Benchmarking short-read metagenomics tools for removing host contamination
• Novel adaptive immune systems in pristine Antarctic soils
• Expansion, restructuring and characterization of the Legionellaceae family
• Origin and transport of bacterial hopanoids
• Essential nucleic acid omics: a theoretical foundation for early-stage users
• Sulfurimonas lacustris sp. nov. and Sulfurimonas limnophila sp. nov. from the chemocline of a meromictic brackish lake
• The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome
• Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth
• High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome
• Genome Mining Guided Identification of the Metallophore Delftichelin A from Delftia deserti
• Immune-microbiome coordination defines interferon setpoints in healthy humans
• The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils
• Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis
• A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
• Complete genome sequence of Rahnella sp. PAMC25559, a psychrophilic plant growth-promoting bacterium isolated from an Alpine glacier
• A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients
• Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier
• Characterization of Staphylococcus argenteus in Christchurch, New Zealand, and comparison to global strains
• A novel cable bacteria species with a distinct morphology and genomic potential
• Isolation and characterization of Sporomusa carbonis sp. nov.: a carboxydotrophic hydrogenogen in the genus of Sporomusa isolated from a charcoal-burning pile
• Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific
• AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
• Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts including clinically relevant species
• Dokdonella aquatica sp. nov., isolated from freshwater
• Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities
• Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses
• Genome sequences of distinct genotypes of bacterial pathogen Xanthomonas euvesicatoria pv. euvesicatoria from pepper (Capsicum annuum L.) in Serbia
• Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia
• Metagenomics reveals fibre fermentation and AMR pathways in red grouse ( Lagopus scotica ) microbiota
• High-resolution metagenome assembly for modern long reads with myloasm
• Decoding the genomic landscape of Mammaliicoccus sp. RAM2 isolated from flacherie-infected Bombyx mori L.
• A holistic genome dataset of bacteria and archaea of mangrove sediments
• Evidence of a novel sublineage of Streptococcus agalactiae in elephants from zoo populations in Germany
• Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats
• The Microflora Danica atlas of Danish environmental microbiomes
• Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism
• Enhancing genome recovery across metagenomic samples using MAGmax
• Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont
• A geological timescale for bacterial evolution and oxygen adaptation
• High-quality metagenome assembly from nanopore reads with nanoMDBG
• Isolation of a putative sulfur comproportionating microorganism
• Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Novel pMMO Diversity
• Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
• Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov.
• Physiological stress response to sulfide exposure of freshwater anaerobic methanotrophic archaea
• The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
• Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter
• First comparative genomics analysis of Corynebacterium auriscanis
• Ningiella algicola sp. nov. and Marinicella algicola sp. nov., proposal of Paralteromonas gen. Nov. and Neoalteromonas gen. Nov. with reclassification of Alteromonas species, and reclassification of Methylophaga aminisulfidivorans as a later heterotypic synonym of Methylophaga thalassica