Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

Cell, Год журнала: 2016, Номер 167(6), С. 1469 - 1480.e12

Опубликована: Дек. 1, 2016

Язык: Английский

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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

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

Опубликована: Дек. 1, 2018

The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence contaminants—DNA sequences not truly present in sample. Contaminants come various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure identifies contaminants MGS data two widely reproduced patterns: appear at higher frequencies low-concentration samples are often found negative controls. Decontam classified amplicon sequence variants (ASVs) human oral dataset consistently with prior microscopic observations taxa inhabiting environment previous reports contaminant taxa. In metagenomics measurements dilution series, substantially reduced technical variation arising different protocols. application to recently published datasets corroborated extended their conclusions little evidence existed for indigenous placenta microbiome some low-frequency seemingly associated preterm birth were contaminants. improves quality by identifying removing DNA sequences. integrates easily existing workflows allows researchers generate more accurate profiles communities no additional cost.

Язык: Английский

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A communal catalogue reveals Earth’s multiscale microbial diversity

Nature, Год журнала: 2017, Номер 551(7681), С. 457 - 463

Опубликована: Окт. 31, 2017

Abstract Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding its fundamental structure. Despite recent advances in DNA sequencing, a lack standardized protocols common analytical frameworks impedes comparisons among studies, hindering development global inferences about life on Earth. Here we present meta-analysis community samples collected by hundreds researchers for Earth Microbiome Project. Coordinated new methods, particularly use exact sequences instead clustered operational taxonomic units, enable bacterial archaeal ribosomal RNA gene to be followed across multiple studies allow us explore patterns at an unprecedented scale. The result is both reference database giving context sequence data framework incorporating from future fostering increasingly complete characterization Earth’s diversity.

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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Microplastics affect sedimentary microbial communities and nitrogen cycling

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Май 12, 2020

Abstract Microplastics are ubiquitous in estuarine, coastal, and deep sea sediments. The impacts of microplastics on sedimentary microbial ecosystems biogeochemical carbon nitrogen cycles, however, have not been well reported. To evaluate if influence the composition function communities, we conducted a microcosm experiment using salt marsh sediment amended with polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF) or polylactic acid (PLA) microplastics. We report that presence alters community cycling processes. Compared to control sediments without microplastic, PUF- PLA-amended promote nitrification denitrification, while PVC amendment inhibits both These results indicate processes can be significantly affected by different microplastics, which may serve as organic substrates for communities. Considering this evidence increasing microplastic pollution, impact plastics global merits critical investigation.

Язык: Английский

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Regional variation limits applications of healthy gut microbiome reference ranges and disease models

Nature Medicine, Год журнала: 2018, Номер 24(10), С. 1532 - 1535

Опубликована: Авг. 17, 2018

Язык: Английский

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The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

Nature, Год журнала: 2019, Номер 574(7777), С. 264 - 267

Опубликована: Окт. 2, 2019

Язык: Английский

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Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

PLoS Computational Biology, Год журнала: 2017, Номер 13(2), С. e1005404 - e1005404

Опубликована: Фев. 21, 2017

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey hierarchical structure taxonomic classifications and are limited for categories. As alternative, we developed metacoder, R package easily parsing, manipulating, graphing publication-ready plots data. Metacoder includes a dynamic flexible function can parse most text-based formats contain classifications, taxon names, identifiers, sequence identifiers. then subset, sample, order this parsed data using set intuitive functions take into account nature Finally, extremely plotting enables quantitative representation up 4 arbitrary statistics simultaneously in tree format mapping size nodes edges. also allows exploration barcode primer bias integrating run digital PCR. Although it has been designed from research, metacoder be applied any component such gene ontology geographic location Our complements currently available tools community analysis provided open source with extensive online user manual.

Язык: Английский

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Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

mSystems, Год журнала: 2017, Номер 2(1)

Опубликована: Янв. 4, 2017

Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa a myriad of factors. A drawback these is that the necessary library preparation bioinformatic analyses complicated continuously changing, which can be barrier for researchers new field. We present three essential components conducting microbiome experiment from start finish: first, simplified step-by-step custom protocol requires limited lab equipment, cost-effective, has been thoroughly tested utilized on various sample types; second, series scripts integrate commonly used tools available standalone installation or single downloadable virtual image; third, set workflows tutorials provide guidance education those This resource will foundations newly entering field much-needed best practices ensure quality research undertaken. All protocols, scripts, workflows, tutorials, images freely through Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki). IMPORTANCE As continues grow, multitude learning how conduct proper experiments. outline here streamlined approach processing samples detailed construction standard operating procedures. allows rapid reliable analysis, allowing focus more their design results. Our bundled software Helper. evolve, updated with training materials.

Язык: Английский

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Bifidobacteria-mediated immune system imprinting early in life

Cell, Год журнала: 2021, Номер 184(15), С. 3884 - 3898.e11

Опубликована: Июнь 17, 2021

Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that turn benefit host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare modern societies. Here we show a lack bifidobacteria, particular depletion genes required for human milk oligosaccharide (HMO) utilization from metagenome, is associated systemic inflammation dysregulation life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) Th17 cytokines were silenced interferon β (IFNβ) was induced. Fecal water EVC001-supplemented contains abundant indolelactate B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 Th2 cells during polarization, functional link between beneficial immunoregulation first months

Язык: Английский

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