MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Uritskiy, Gherman; DiRuggiero, Jocelyne; Taylor, James

doi:10.1101/277442

Cited by 153 publications

(216 citation statements)

References 54 publications

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“…Following quality trimming (Trimmomatic v 0.39; Bolger et al ), with reads shorter than 20 bp being discarded and removal of human genes (MetaWRAP; Uritskiy et al ), the clean metagenomic data were assembled into contigs by de novo assembly of each sample sequence using metaSPAdes (SPAdes v.3.13.0; Bankevich et al ). The interactome (i.e., Microcystis and its microbiome) metagenomic assembled genomes (MAGs) were generated for each lake using three tools with default options: MaxBin (v.2.2.6) (Wu et al ), MetaBAT (v. 2.12.1) (Kang et al ), and CONCOCT (v. 1.0.0) (Alneberg et al unpubl.…”

Section: Methodsmentioning

confidence: 99%

The global Microcystis interactome

Cook

Cai

et al. 2019

Limnology & Oceanography

100

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Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280 longitudinal and 90 latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.

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Section: Methodsmentioning

confidence: 99%

The global Microcystis interactome

Cook

Cai

et al. 2019

Limnology & Oceanography

100

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“…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

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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“…Bins with a completeness ≥ 50% and contamination ≤ 10% were considered to be “high quality” and were used in the subsequent analyses. (3) The raw abundance ( A j ) of a specific bin in a given sample j was calculated using metaWRAP (Uritskiy et al ) with the following formula:

A_{j} = \frac{\sum_{i = 1}^{N} l_{i} c_{ij}}{\sum_{i = 1}^{N} l_{i}}

…”

Section: Methodsmentioning

confidence: 99%

Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake

Xing

Tao

Luo

et al. 2019

Limnology & Oceanography

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In warm monomictic lakes, the hypolimnion is important for accumulating and decomposing organic matter derived from surface production, and the regenerated nutrients will be supplied to the epilimnion through winter vertical mixing. So far, we know little about microbial community composition and function in the hypolimnion when the significant thermal stratification disappears. In this study, we investigated microbial community compositions and functional gene contents by means of metagenomics along a depth profile in the warm monomictic alpine Lake Fuxian during holomictic period. Overall, bacteria were the dominant microbial group at different water depths, while phages had their high relative abundance in the epilimnion. We observed slight thermal but strong chemical stratification even during this typical winter overturn. The anaerobic respiration with nitrate and sulfate as the terminal electron acceptors was accumulated at bottom of hypolimnionin as indicated through metabolic pathway reconstruction. We were able to get 440 metagenome-assembled genomes (MAGs) and unraveled a high genomic diversity of freshwater pelagic microbiomes along this depth profile. We furthermore defined a new class of "Plancto_FXH1" of Planctomycetes from these MAGs, of which a distinct nitrate reduction operon was identified. Representatives of this phylum mainly thrive in the hypolimnion as previously suspected, but few lineages were detected in the epilimnion. In summary, metagenomics enabled us to find a new group of Planctomycetes, probably involved in denitrification in the hypolimnion in Lake Fuxian, which expand our knowledge on denitrifying bacterial diversity and their denitrification potential in deep freshwater lakes.

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MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Cited by 153 publications

References 54 publications

The global Microcystis interactome

The global Microcystis interactome

Accurate and Complete Genomes from Metagenomes

Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake

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