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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Clinical metagenomics

Nature Reviews Genetics, Год журнала: 2019, Номер 20(6), С. 341 - 355

Опубликована: Март 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.

Язык: Английский

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FROGS: Find, Rapidly, OTUs with Galaxy Solution

Bioinformatics, Год журнала: 2017, Номер 34(8), С. 1287 - 1294

Опубликована: Дек. 5, 2017

Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools analyze their data on own.This Galaxy-supported pipeline, called FROGS, is designed large sets of amplicon sequences produce abundance tables Operational Taxonomic Units (OTUs) taxonomic affiliation. The clustering uses Swarm. chimera removal VSEARCH, combined with original cross-sample validation. affiliation returns an innovative multi-affiliation output highlight databases conflicts uncertainties. Statistical results numerous graphical illustrations are produced along the way monitor pipeline. FROGS was tested for detection quantification OTUs real silico datasets proved be rapid, robust highly sensitive. It compares favorably widespread mothur, UPARSE QIIME.Source code instructions installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://[email protected] available at Bioinformatics online.

Язык: Английский

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Culturing the human microbiota and culturomics

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(9), С. 540 - 550

Опубликована: Июнь 24, 2018

Язык: Английский

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Simplified and representative bacterial community of maize roots

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(12)

Опубликована: Март 8, 2017

Plant-associated microbes are important for the growth and health of their hosts. As a result numerous prior studies, we know that host genotypes abiotic factors influence composition plant microbiomes. However, high complexity these communities challenges detailed studies to define experimentally mechanisms underlying dynamics community assembly beneficial effects such microbiomes on In this work, from distinctive microbiota assembled by maize roots, through host-mediated selection, obtained greatly simplified synthetic bacterial consisting seven strains (Enterobacter cloacae, Stenotrophomonas maltophilia, Ochrobactrum pituitosum, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum, Chryseobacterium indologenes) representing three four most dominant phyla found in roots. By using selective culture-dependent method track abundance each strain, investigated role plays roots axenic seedlings. Only removal E. cloacae led complete loss community, C. pusillum took over. This suggests keystone species model ecosystem. planta vitro, inhibited phytopathogenic fungus Fusarium verticillioides, indicating clear benefit host. Thus, combined with quantification method, our seven-species root microbiome has potential serve as useful system explore how interspecies interactions affect dissect hosts under laboratory conditions future.

Язык: Английский

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The Epidemiology of Esophageal Adenocarcinoma

Gastroenterology, Год журнала: 2017, Номер 154(2), С. 390 - 405

Опубликована: Авг. 3, 2017

Язык: Английский

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Health Benefits of Heat-Killed (Tyndallized) Probiotics: An Overview

International Journal of Molecular Sciences, Год журнала: 2019, Номер 20(10), С. 2534 - 2534

Опубликована: Май 23, 2019

Nowadays, the oral use of probiotics is widespread. However, safety profile with live still a matter debate. Main risks include: Cases systemic infections due to translocation, particularly in vulnerable patients and pediatric populations; acquisition antibiotic resistance genes; or interference gut colonization neonates. To avoid these risks, there an increasing interest non-viable microorganisms microbial cell extracts be used as probiotics, mainly heat-killed (including tyndallized) probiotic bacteria (lactic acid bifidobacteria). Heat-treated cells, cell-free supernatants, purified key components are able confer beneficial effects, immunomodulatory protection against enteropathogens, maintenance intestinal barrier integrity. At clinical level, products containing tyndallized strains have had role gastrointestinal diseases, including bloating infantile coli—in combination mucosal protectors—and diarrhea. Heat-inactivated could also management dermatological respiratory allergic diseases. The reviewed data indicate that their fractions advantages versus (mainly profile), positioning them interesting strategies for common prevalent conditions wide variety patients´ characteristics.

Язык: Английский

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Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

Nature Biotechnology, Год журнала: 2017, Номер 35(11), С. 1077 - 1086

Опубликована: Окт. 2, 2017

Язык: Английский

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Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota

Frontiers in Microbiology, Год журнала: 2018, Номер 9

Опубликована: Сен. 11, 2018

Stress, a ubiquitous part of daily human life, has varied biological effects which are increasingly recognized as including modulation commensal microorganisms residing in the gastrointestinal tract, gut microbiota. In turn, microbiota influences host stress response and associated sequelae, thereby implicating an important mediator health. This narrative review aims to synthesize evidence concerning impact psychological, environmental, physical stressors on composition activity. The reviewed include psychological stress, circadian disruption, sleep deprivation, environmental extremes (high altitude, heat, cold), pathogens, toxicants pollutants, activity, diet (nutrient food restriction). Stressors were selected for their direct relevance military personnel, population that is commonly exposed these stressors, often at extremes, combination. However, also common, alone or combination, some civilian populations. Evidence from preclinical studies collectively indicates alter but vary across can may be beneficial detrimental Translation findings humans largely lacking present. gap precludes concluding with certainty transient cumulative exposures have any consistent, meaningful provocative highlights need translational research aiming elucidate microbiota, how manipulated, example by using nutrition, mitigate adverse responses.

Язык: Английский

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Inflammation–Nature's Way to Efficiently Respond to All Types of Challenges: Implications for Understanding and Managing “the Epidemic” of Chronic Diseases

Frontiers in Medicine, Год журнала: 2018, Номер 5

Опубликована: Ноя. 27, 2018

Siloed or singular system approach to disease management is common practice, developing out of traditional medical school education. Textbooks medicine describe a huge number discrete diseases, usually in systematic fashion following headings like etiology, pathology, investigations, differential diagnoses, and management. This suggests that the body has multitude ways respond harmful incidences. However, physiology systems biology provide evidence there simple mechanism behind this phenotypical variability. Regardless if an injury change was caused by trauma, infection, non-communicable disease, autoimmune disorders, stress, typical physiological response is: increase blood supply area, white cells into affected tissue, phagocytic activity remove offending agent, followed down-regulation these mechanisms resulting healing. The cascade inflammation body's unique maintain its integrity macroscopic as well microscopic injuries. We hypothesize chronic development progression are linked uncontrolled dysfunctional injuries regardless their nature, physical, environmental, psychological. Thus, we aim reframe prevailing individual diseases more integrated systemic treating "person whole," enhancing patient experience, ability make necessary changes, maximize overall health well-being. first part paper reviews local immune cascades pro- anti-inflammatory regulation interconnected feedback loops with neural psychological pathways. second emphasizes one nature's principles at work-system design efficiency. Continually overwhelming finely tuned will result allowing emerge; pathways several conditions described detail. final considers implications understandings for clinical care explore how lens could shape physician-patient encounter redesign. conclude healthcare professionals must advocate lifestyle level national levels enhance population

Язык: Английский

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