MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

PeerJ, Год журнала: 2019, Номер 7, С. e7359 - e7359

Опубликована: Июль 26, 2019

We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated species. MetaBAT has become one the most popular tools largely due its computational efficiency and ease use, especially in experiments with a large number samples assembly. requires users choose parameters fine-tune sensitivity specificity. If those are not chosen properly, accuracy can suffer, assemblies poor quality. Here, we developed 2 overcome this problem. uses new adaptive algorithm eliminate manual parameter tuning. also performed extensive engineering optimization increase both memory efficiency. Comparing alternative over 100 real world shows superior computing speed. Binning typical assembly takes only few minutes commodity workstation. therefore recommend community adopts their experiments. is open source available at https://bitbucket.org/berkeleylab/metabat.

Язык: Английский

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MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

Bioinformatics, Год журнала: 2015, Номер 32(4), С. 605 - 607

Опубликована: Окт. 29, 2015

Abstract Summary: The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput microbial metagenomes. Here we present expanded algorithm, MaxBin 2.0, which recovers co-assembly collection datasets. Tests on simulated revealed that 2.0 highly accurate in recovering individual genomes, and application several metagenomes environmental samples demonstrated it could achieve two complementary goals: more bacterial compared single sample as well comparing community composition between different sampling environments. Availability implementation: freely available at http://sourceforge.net/projects/maxbin/ under BSD license. Contact: [email protected] Supplementary information: data are Bioinformatics online.

Язык: Английский

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Structure and function of the global topsoil microbiome

Nature, Год журнала: 2018, Номер 560(7717), С. 233 - 237

Опубликована: Июль 31, 2018

Язык: Английский

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

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Сен. 15, 2018

The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic at single genome level. Software and pipelines for such become diverse sophisticated, resulting a significant burden biologists to access use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still lack tools evaluation visualization. To address these challenges, we present metaWRAP, modular pipeline software data analysis. MetaWRAP deploys state-of-the-art handle processing starting from raw reads ending bins flexible enough give investigators control over analysis, being easy-to-install easy-to-use. It includes hybrid leverage strengths variety extract refine high-quality through consolidation reassembly. MetaWRAP's algorithm outperforms binning approaches other programs both synthetic real sets. Finally, metaWRAP comes with numerous modules bins, including taxonomy assignment, abundance estimation, functional annotation, an easy-to-use automates core tasks contributing improvements interpretation bins. refinement reassembly consistently outperform approaches. Each module also standalone component, making it versatile tool tackling data. open-source available https://github.com/bxlab/metaWRAP .

Язык: Английский

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

Nature Microbiology, Год журнала: 2017, Номер 2(11), С. 1533 - 1542

Опубликована: Сен. 11, 2017

Abstract Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances sequencing throughput and computational techniques that allow for cultivation-independent recovery genomes from metagenomes. Here, we report reconstruction 7,903 bacterial archaeal >1,500 public All are estimated to be ≥50% complete nearly half ≥90% with ≤5% contamination. These increase genome trees >30% provide first representatives 17 three candidate phyla. We also recovered 245 Patescibacteria superphylum (also known as Candidate Phyla Radiation) find relative this group varies substantially different protein marker sets. The scale quality data set demonstrate recovering metagenomes provides an expedient path forward exploring dark matter.

Язык: Английский

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Anvi’o: an advanced analysis and visualization platform for ‘omics data

PeerJ, Год журнала: 2015, Номер 3, С. e1319 - e1319

Опубликована: Окт. 8, 2015

Advances in high-throughput sequencing and 'omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations lifestyles require the ability to interactively organize visualize genetic information incorporate subtle differences that enable greater resolution complex data. Here we introduce anvi'o, an advanced analysis visualization platform offers automated human-guided characterization genomes metagenomic assemblies, with interactive interfaces can link data from multiple sources into a single, intuitive display. Its extensible approach distills dimensions about each contig, offering dynamic unified work environment for exploration, manipulation, reporting. Using re-analyzed publicly available datasets explored temporal genomic changes within populations through de novo single nucleotide variations, linked cultivar single-cell metatranscriptomic Anvi'o is open-source empowers researchers without extensive bioinformatics skills perform communicate in-depth analyses on large datasets.

Язык: Английский

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Shotgun metagenomics, from sampling to analysis

Nature Biotechnology, Год журнала: 2017, Номер 35(9), С. 833 - 844

Опубликована: Сен. 1, 2017

Язык: Английский

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Cell, Год журнала: 2019, Номер 176(3), С. 649 - 662.e20

Опубликована: Янв. 1, 2019

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% high quality) spanning body sites, ages, countries, lifestyles. recapitulated 4,930 species-level genome bins (SGBs), 77% without public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% well-assembled samples), expand underrepresented phyla, enriched non-Westernized populations (40% total SGBs). annotated 2.85 M genes SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). permit deeper analyses increase average mappability metagenomic reads from 67.76% 87.51% (median 94.26%) 65.14% 82.34% mouth. thus identify thousands yet-to-be-named species, pangenomes human-associated microbes, allow better exploitation technologies.

Язык: Английский

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

Nature Microbiology, Год журнала: 2018, Номер 3(7), С. 836 - 843

Опубликована: Май 25, 2018

Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment assembled genome fragments genomes. Existing binning methods often fail a reasonable number genomes report many bins low quality completeness. Furthermore, the performance existing algorithms varies between samples biotopes. Here, we present dereplication, aggregation scoring strategy, DAS Tool, that combines strengths flexible set established algorithms. Tool applied constructed generated more than any automated method. Indeed, when environmental host-associated different complexity, recovered substantially near-complete genomes, including previously unreported lineages, single method alone. The ability from metagenomics data will greatly advance genome-centric analyses ecosystems.

Язык: Английский

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A new genomic blueprint of the human gut microbiota

Nature, Год журнала: 2019, Номер 568(7753), С. 499 - 504

Опубликована: Фев. 11, 2019

The composition of the human gut microbiota is linked to health and disease, but knowledge individual microbial species needed decipher their biological roles. Despite extensive culturing sequencing efforts, complete bacterial repertoire remains undefined. Here we identify 1,952 uncultured candidate by reconstructing 92,143 metagenome-assembled genomes from 11,850 microbiomes. These substantially expand known collective microbiota, with a 281% increase in phylogenetic diversity. Although newly identified are less prevalent well-studied populations compared reference isolate genomes, they improve classification understudied African South American samples more than 200%. encode hundreds biosynthetic gene clusters possess distinctive functional capacity that might explain elusive nature. Our work expands diversity bacteria, which provides unprecedented resolution for taxonomic characterization intestinal microbiota.

Язык: Английский

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