CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.; Hugenholtz, Philip; Tyson, Gene W.

doi:10.7287/peerj.preprints.554v1

Cited by 427 publications

(563 citation statements)

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“…We predominantly considered environmental and nonhuman gastrointestinal samples in order to focus on metagenomes likely to contain microbial populations from under-sampled lineages (Supplementary Table 1). The completeness and contamination of each MAG was estimated from the presence and absence of lineage-specific genes expected to be ubiquitous and single copy 25 , and these estimates, along with assembly statistics, used to identify genomes suitable for further study. A total of 64,295 MAGs were obtained, of which 7,903 (7,280 bacterial and 623 archaeal)…”

Section: Resultsmentioning

confidence: 99%

“…The correlation between estimated genome completeness and identified tRNAs was positive but weak ( Supplementary Fig. 2) as tRNAs are regularly present in multiple copies and often collocated in a genome, making them poor markers for robustly estimating completeness 25,38 .Taxonomic distribution of UBA genomes. The phylogenetic relationships of the UBA genomes were determined across bacterial and archaeal trees inferred from three concatenated protein sets: (1) a syntenic block of 16 ribosomal proteins (rp1) recently used to infer genome-based phylogenies 10,30 (Supplementary Table 4), (2) 23 ribosomal proteins (rp2) previously tested for lateral gene transfer 4 (Supplementary Table 5), and (3) 120 bacterial (bac120) and 122 archaeal (ar122) proteins we have identified as being suitable for phylogenetic inference (Supplementary Tables 6 and 7).…”

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confidence: 99%

“…Although closed genomes have been obtained using metagenomic binning methods 10,23 , MAGs are typically incomplete and may contain contigs from multiple strains or species due to challenges in distinguishing between related community members both in the assembly and binning processes 19,24 . This has spurred the development of methods for assessing the quality of recovered MAGs in order to allow biological inferences to be made with regards to their estimated completeness and contamination 25,26 .…”

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

et al. 2017

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Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from > 1,500 public metagenomes. All genomes are estimated to be ≥ 50% complete and nearly half are ≥ 90% complete with ≤ 5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by > 30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter. Articles NATuRe MiCRobiologyform the UBA data set as they met our filtering criteria of having an estimated quality ≥ 50 (defined as the estimated completeness of a genome minus five times its estimated contamination) and consisting of ≤ 500 scaffolds with an N50 ≥ 10 kb ( Fig. 1 and Supplementary Table 2). Over 93% of the 7,903 UBA genomes have an average coverage of ≥ 10× (5th percentile, 9.2× , 95th percentile, 268× ) and 95.8% have > 5× coverage over 90% of bases, providing assurance of high-quality base-calling across the genomes 3,36 . Among the UBA genomes is a subset of 3,438 near-complete genomes (3,225 bacterial and 213 archaeal) estimated to be ≥ 90% complete with ≤ 5% contamination (Fig. 1a). These genomes consist of ≤ 100 scaffolds in 70.2% of cases (≤ 200 scaffolds in 92.0% genomes) and have an average N50 of 136 kb. Comparison of near-complete UBA genomes that are conspecific strains of complete isolate genomes also suggest that the recovered MAGs have no systematic loss of genomic content, with the exception of extrachromosomal elements such as plasmids (Supplementary Note 1).The UBA data set was also assessed relative to the criteria used by the Human Microbiome Project (HMP) for defining high-quality draft genomes 3,37 . Of the 3,438 UBA genomes we have defined as near complete, 3,201 (93.1%) pass all of the HMP criteria, with the only substantial exception being 4.8% of the genomes having scaffolds with an N50 of < 20 kb (Supplementary Table 3). Nearly half of the remaining 4,465 UBA genomes also pass the HMP criteria for being high quality except that they are estimated to be < 90% complete.The presence of tRNAs for the standard 20 amino acids was examined as a secondary measure of genome quality (Fig. 1c). The 3,438 near-complete UBA genomes have tRNAs that encode for an average of 17.3 ± 2.2 of the 20 amino acids and ≥ 15 amino acids in 90.3% of the genomes. The correlation between estimated genome completeness and identified tRN...

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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“…This list of single-copy genes has been used to estimate genome completeness in several recent studies 13,63 . When we analysed the genome using another metric of genome completeness (checkM 64 ), the results suggested that the genome was 80% complete with 4% contamination, a level categorized as a 'substantially complete draft with low contamination'. This level of completeness is similar to several other recent genomes assembled from metagenomes 65,66 .…”

Section: Methodsmentioning

confidence: 99%

“…This level of completeness is similar to several other recent genomes assembled from metagenomes 65,66 . However, because checkM relies on lineage-specific marker genes, the completeness of genomes without lineage representation can often be underestimated 64 . As there is only one complete genome for the entire class Spartobacteria (C. flavus), the checkM genome completeness estimate for Ca.…”

Section: Methodsmentioning

confidence: 99%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

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Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘Candidatus Udaeobacter copiosus’. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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Recovering Individual Genomes from Metagenomes Using MaxBin 2.0

Singer

2021

Current Protocols

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It is critical to identify individual genomes from microbiomic samples in order to carry out analysis of the microbes. Methods based on existing databases, however, may have limited capabilities in elucidating and quantifying the microbes due to the largely unidentified microbial species in natural or humanassociated environments. We thus developed a database-free method, MaxBin 2.0, to aid in the process of recovering microbial genomes from metagenomes in a de novo manner. The recovery of individual genomes allows analysis of the microbiome in terms of a collection of microbial genomes so that one can understand the functional roles of each species. The data of individual microbes may then be analyzed collectively to untangle the interactions between different microbial organisms. By reporting the genome abundance information for co-assembled metagenomes, one may also identify which microorganisms dominate the microbiome and which species may co-occur from the MaxBin 2.0 results.

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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Cited by 427 publications

References 14 publications

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Recovering Individual Genomes from Metagenomes Using MaxBin 2.0

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