Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison; Thomas, Brian C.; Hess, Matthias; Tringe, Susannah G.; Banfield, Jillian F.

doi:10.1038/s41564-018-0171-1

Cited by 1,066 publications

(894 citation statements)

References 40 publications

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“…Reads were mapped to scaffolds with bowtie2 (Langmead and Salzberg, ) to determine their relative abundance. Automated binning was conducted with Metabat (Kang et al ., ) and Concoct (Alneberg et al ., ) using differential coverage information and the best genomic bins were selected with DAStool (Sieber et al ., ). Bins were imported into ggKbase (https://ggkbase.berkeley.edu) for further manual refinement based on their GC, coverage, taxonomy of scaffolds, as well as completion assessed according to the number of bacterial single copy genes present in each bin.…”

Section: Methodsmentioning

confidence: 97%

“…Reads were mapped to scaffolds with bowtie2 (Langmead and Salzberg, 2012) to determine their relative abundance. Automated binning was conducted with Metabat (Kang et al, 2015) and Concoct (Alneberg et al, 2014) using differential coverage information and the best genomic bins were selected with DAStool (Sieber et al, 2018). Bins were imported into ggKbase (https://ggkbase.berkeley.…”

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

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Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Poghosyan

Koch

Lavy

et al. 2019

Environmental Microbiology

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Summary The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high‐quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome‐assembled genomes were compared with other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clades A and B respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I–V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clades A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated.

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Section: Methodsmentioning

confidence: 97%

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Poghosyan

Koch

Lavy

et al. 2019

Environmental Microbiology

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“…We have found that no single binning algorithm is the most effective for all 153 sample/environment types or even for all populations within one sample. The recently published method 154 DASTool tests a flexible number of different binning methods, evaluates all outcomes and chooses the best bin 155 for each population (Sieber et al 2018). A similar strategy has been utilized in a modular pipeline software 156 called MetaWRAP (Uritskiy et al 2018).…”

Section: Running Title: Curated and Complete Metagenome-assembled Genmentioning

confidence: 99%

Accurate and Complete Genomes from Metagenomes

Chen

Anantharaman

Shaiber

et al. 2019

Preprint

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127

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51Genomes are an integral component of the biological information about an organism and, logically, the more 52 complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were 53 reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to 54 completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights 55 for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as 56 community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation 57 by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and 58 contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome 59 curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few 60 CMAGs have been generated, although notably some are from very complex systems such as soil and 61 sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of 62 cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. 63Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes 64 of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could 65 be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary 66 analyses can be based on very high-quality genomes. 67 68 69 70 2017), and even human blood (Moustafa et al. 2017) amenable to shotgun metagenomic surveys and recovery 87 of MAGs. Although incomplete, draft MAGs represent a major advance over knowing nothing about the genes 88 and pathways present in an organism, and led to the discovery of new metabolisms. For example, the complete 89 oxidation of ammonia to nitrate via nitrite (i.e., comammox) was determined by the detection of necessary 90 genes in a single MAG (Daims et al. 2015; van Kessel et al. 2015). MAGs are often derived from uncultivated 91 organisms that can be quite distantly related to any isolated species, which is a clear advantage of MAGs 92 (Becraft et al. 2017; Garg et al. 2019). For this reason, genome-resolved metagenomics has been critical for 93 more comprehensive descriptions of bacterial and archaeal diversity and the overall topology of the Tree of 94

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“…The sequence mapping files were processed using SAMtools 1.6 (Li et al 2009 (Kang et al 2015). The four bin sets were supplied to DAS Tool 1.0 (Sieber et al 2018) for consensus binning to obtain the final bins. The quality of the genome bins was assessed through a single-copy marker gene analysis using CheckM 1.0.7 .…”

Section: Rasigraf Et Almentioning

confidence: 99%

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

Rasigraf

Helmond

Frank

et al. 2019

Limnology & Oceanography

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The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane, and ammonium in its sediments, enabling the activity and interactions of many microbial guilds. Here, we studied the microbial network in these sediments by analyzing geochemical and microbial community depth profiles at one offshore and two near coastal sites. Analysis of 16S rRNA gene amplicons revealed a distinct depth stratification of both archaeal and bacterial taxa. The microbial communities at the two near coastal sites were more similar to each other than the offshore site, which is likely due to differences in the quality and rate of organic matter degradation. The abundance of methanotrophic archaea of the ANME-2a clade was shown to be related to the presence of methane and varied with sediment iron content. Metagenomic sequencing of sediment-derived DNA from below the sulfate-methane transition zone revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. The potential for nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene-centric fermentative metabolism analysis indicated a potential importance for acetate, formate, alcohol, and hydrogen metabolism. Methanogenic/-trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae, and ANME-2 archaea. Our results indicated flexible metabolic capabilities of core microbial community taxa, which could adapt to changing redox conditions, and with a spatial and depth distribution that is likely governed by the quality and input of available organic substrates and, for ANME-2, of iron oxides.

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Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Cited by 1,066 publications

References 40 publications

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Accurate and Complete Genomes from Metagenomes

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

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