A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D.; Pati, Amrita; Lykidis, Athanasios; Spring, Stefan; Anderson, Iain; D’haeseleer, Patrik; Zemła, Adam; Singer, Mitchell; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Han, Cliff; Chen, Feng; Cheng, Jan‐Fang; Lucas, Susan; Kerfeld, Cheryl A.; Lang, Elke; Gronow, Sabine; Chain, Patrick; Bruce, David; Rubin, Edward M.; Kyrpides, Nikos C.; Klenk, Hans Peter; Eisen, Jonathan A.

doi:10.1038/nature08656

Cited by 899 publications

(884 citation statements)

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“…Consequently, current genome repositories are not representative of the microbial diversity known from 16S rRNA gene surveys 4 . Concerted efforts are being made to address this limitation by target ing phylogenetically distinct microorganisms for cultivation [5][6][7] and single-cell sequencing 4,8 . Although these approaches continue to provide valuable reference genomes, the former is restricted to microorganisms amenable to cultivation and the latter is hampered by technical challenges and the need for specialised equipment 9 .…”

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confidence: 99%

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

et al. 2017

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“…Simulated genomes were generated from 2430 draft with each draft genome being used to generate 20 simulated genomes with a completeness of 50%, 70%, 80%, or 90% and contamination of 5%, 10%, Albertsen et al (2013) References: GEBA (Wu et al 2009), GEBA-PCC (Shih et al 2012), HMP (Turnbaugh et al 2007), GEBA-MDM (Rinke et al 2013), IMG (Markowitz et al 2014), Sludge bioreactor (Albertsen et al 2013), Acid mine drainage (Tyson et al 2004), Infant gut ), Acetate-amended aquifer (Wrighton et 745 al. 2012), IMG (Markowitz et al 2014).…”

Section: Genome Datasetsmentioning

confidence: 99%

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

Parks

Imelfort

Skennerton

et al. 2014

Preprint

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Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While 25 this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of 'marker' genes conserved across all bacterial or archaeal 30 genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate, single cell and metagenome derived genomes. CheckM is shown to provide accurate estimates of genome completeness and 35 contamination, and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene-and genome-centric analyses of microbial communities. CheckM is open 40 source software available at http://ecogenomics.github.io/CheckM.

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“…272 species of bacteria and archaea, whose genomes have been completely sequenced and are available at NCBI, were chosen so as to cover the full diversity of bacterial and archaeal lineages (Wu et al, 2009) (http://tolweb.org/tree/) and the full bioenergetic diversity per lineage, as previously described (Koumandou and Kossida, 2014). For lineages with many sequenced genomes, the tree of (Wu et al, 2009) was used to pick species so as to cover as much phylogenetic diversity as possible with a limited number of species.…”

Section: Organism Selectionmentioning

confidence: 99%

“…For lineages with many sequenced genomes, the tree of (Wu et al, 2009) was used to pick species so as to cover as much phylogenetic diversity as possible with a limited number of species. The set of species selected represent 131 clusters with a genome similarity score (GSS) threshold of 0.5 (Moreno-Hagelsieb et al, 2013); of those, 24 belong to single-species "clusters", and 63 are the sole representatives from their cluster.…”

Section: Organism Selectionmentioning

confidence: 99%

Evolution of b-type cytochromes in prokaryotes

Koumandou

Κοσσίδα

2015

Preprint

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Abstract:Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b 6 f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fehydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b 6 f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b 6 ; also, the split form of b 6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.PeerJ PrePrints | https://doi.org/10.7287/peerj.preprints.1564v1 | CC-BY 4.0 Open Access |

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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Cited by 899 publications

References 30 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

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

Evolution of b-type cytochromes in prokaryotes

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