IMG/M 4 version of the integrated metagenome comparative analysis system

Markowitz, Victor; Chen, I-Min A.; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah G.; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia; Kyrpides, Nikos C.

doi:10.1093/nar/gkt919

Cited by 245 publications

(256 citation statements)

References 23 publications

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“…These contrasting views of the diversity of the CPR are equally valid and probably reflect the unique biology of the organisms within this group. While the SRA represents a large set of publicly available metagenomic data, many additional metagenomes exist in other repositories such as the Integrated Microbial Genomes and Metagenomes 49 (IMG/M) database and Metagenomics Rapid Annotation Server 50 (MG-RAST). We expect that processing these metagenomes will add tens of thousands of additional genomes to the tree of life.…”

Section: Nature Microbiologymentioning

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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Section: Nature Microbiologymentioning

confidence: 99%

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

et al. 2017

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“…Bioinformatic Analysis of the Glyoxylate Shunt-To investigate the phylogenetic distribution of the glyoxylate shunt, isocitrate lyase and malate synthase sequences were retrieved using the Gene Search function in the integrated microbial genome (IMG) database (23), which contained 27,319 bacterial genomes as of July 2015. To reduce database redundancy, only one strain was arbitrarily selected for each species when genomic data were available for multiple strains of one species.…”

Section: Measurement Of the Nadh/nadmentioning

confidence: 99%

Role of Glyoxylate Shunt in Oxidative Stress Response

Ahn

Jung

Jang

et al. 2016

Journal of Biological Chemistry

189

154

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The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli. In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N 2 O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.

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“…Both the IMG/M-ER (Markowitz et al, 2014) and RAST (Aziz et al, 2008) platforms were used for gene calling, functional prediction and comparison of SAGs and metagenome bins. Because not all of the data sets could be uploaded to IMG/M-ER, RAST was used as a common platform and annotation system for most comparative analyses; however, IMG/M-ER was useful for checking functional annotations and for gene calling near the ends of open reading frames in these fragmented SAG and metagenome bin data sets.…”

Section: Genomic Analyses and Identification Of Potentially Monophylementioning

confidence: 99%

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

et al. 2015

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The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species-to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

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IMG/M 4 version of the integrated metagenome comparative analysis system

Cited by 245 publications

References 23 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

Role of Glyoxylate Shunt in Oxidative Stress Response

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

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