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

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Sept. 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 .

Language: Английский

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Best practices for analysing microbiomes

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(7), P. 410 - 422

Published: May 23, 2018

Language: Английский

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife, Journal Year: 2021, Volume and Issue: 10

Published: May 4, 2021

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now available. Compared current alternatives, MetaPhlAn 3 increases accuracy taxonomic profiling, HUMAnN improves that functional potential activity. These detected novel disease-microbiome links applications CRC (1262 metagenomes) IBD (1635 817 metatranscriptomes). Strain-level an additional 4077 StrainPhlAn PanPhlAn unraveled structure common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations cloud-deployable reproducible workflows, platform can help researchers deepen resolution, scale, multi-omic community studies.

Language: Английский

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

Cell, Journal Year: 2019, Volume and Issue: 176(3), P. 649 - 662.e20

Published: Jan. 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.

Language: Английский

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Clinical metagenomics

Nature Reviews Genetics, Journal Year: 2019, Volume and Issue: 20(6), P. 341 - 355

Published: March 27, 2019

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA RNA) in samples from patients, is rapidly moving research to clinical laboratories. This emerging approach changing how physicians diagnose treat infectious disease, with applications spanning a wide range areas, including antimicrobial resistance, microbiome, human gene expression (transcriptomics) oncology. Here, we focus on challenges implementing mNGS laboratory address potential solutions for maximizing its impact patient care public health. (mNGS) bench bedside. Review discusses mNGS, disease diagnostics, microbiome analyses, response analyses oncology applications. Moreover, authors review that need be overcome successfully implemented propose maximize benefits patients.

Language: Английский

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A new genomic blueprint of the human gut microbiota

Nature, Journal Year: 2019, Volume and Issue: 568(7753), P. 499 - 504

Published: Feb. 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.

Language: Английский

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Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Cell Host & Microbe, Journal Year: 2018, Volume and Issue: 24(1), P. 133 - 145.e5

Published: July 1, 2018

Language: Английский

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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Feb. 1, 2021

Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, insufficiently advanced identification tools.Here, we introduce VirSorter2, DNA RNA virus tool that leverages genome-informed advances across collection customized automatic classifiers improve accuracy range detection. When benchmarked against genomes from both isolated uncultivated viruses, VirSorter2 uniquely performed consistently with high (F1-score > 0.8) viral diversity, while all other tools under-detected viruses outside group represented reference databases (i.e., those order Caudovirales). Among evaluated, was also able minimize errors associated atypical cellular sequences including eukaryotic plasmids. Finally, as virosphere exploration unravels novel sequences, VirSorter2's modular design makes it inherently expand new types via maintain maximal sensitivity specificity.With multi-classifier design, demonstrates higher overall major groups will advance our knowledge evolution, virus-microbe interaction various ecosystems. Source code is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), on bioconda an iVirus app CyVerse https://de.cyverse.org/de ). Video abstract.

Language: Английский

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IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D666 - D677

Published: Sept. 24, 2018

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source include those generated by the DOE's Joint Genome Institute (JGI), submitted external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through IMG annotation pipeline then loaded into warehouse. IMG's web user interface provides a variety of analytical visualization tools for comparative analysis isolate genomes metagenomes in IMG. IMG/M allows open access to all warehouse, while its expert review (ER) (IMG/MER: https://img.jgi.doe.gov/mer/) registered users their private store workspace sharing further analysis. content has grown 60% since last report published 2017 NAR Database Issue. new more powerful search feature, statistical tools, supports metagenome binning.

Language: Английский

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Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Nature Medicine, Journal Year: 2019, Volume and Issue: 25(4), P. 667 - 678

Published: April 1, 2019

Language: Английский

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