phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

PLoS ONE, Год журнала: 2013, Номер 8(4), С. e61217 - e61217

Опубликована: Апрель 22, 2013

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration different types data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With increased breadth experimental designs now being pursued, project-specific statistical analyses are often needed, these difficult (or impossible) for peer researchers to independently reproduce. vast majority requisite tools performing reproducibly already implemented in R its extensions (packages), but limited support high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated object-oriented representation R. It supports importing variety common formats, as well techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, production publication-quality graphics; all manner that is easy document, share, modify. We show how apply functions other packages phyloseq-represented data, illustrating availability large number open source discuss use phyloseq reproducible research, practice fields still rare highly parallel have made available materials necessary completely reproduce figures included this article, an example best practices research. Conclusions project new open-source package, freely on web both GitHub Bioconductor.

Язык: Английский

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Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

Aquatic Microbial Ecology, Год журнала: 2015, Номер 75(2), С. 129 - 137

Опубликована: Апрель 17, 2015

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout JournalEditorsSpecials 75:129-137 (2015) - DOI: https://doi.org/10.3354/ame01753 Minor revision V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Amy Apprill1,*, Sean McNally1,2, Rachel Parsons2, Laura Weber1 1Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA 2Bermuda Institute Ocean Sciences, Ferry Reach, St. George’s GE01, Bermuda *Corresponding author: [email protected] ABSTRACT: High-throughput sequencing small subunit ribosomal RNA (SSU rRNA) genes from marine environments is a widely applied method used uncover composition microbial communities. We conducted an analysis surface ocean waters with commonly employed hypervariable 4 primers 515F and 806R, found that bacteria belonging clade Alphaproteobacteria, group typically making up 20 40% in this environment, were underrepresented comprised <4% total community. Using SILVA reference database, we single nucleotide mismatch nearly all subclades, revised so it increased sequences database 2.6 96.7%. then compared performance original seawater samples, 0.3 3.9% 17.5 30.5% primer. Furthermore, investigation obtained aquaria revealed acquired more similar natural cellular abundances detected using fluorescence situ hybridization counts. Collectively, these results demonstrate minor adjustment will increase globally abundant lake environments, enable inclusion important bacterial lineage experimental environmental-based studies. KEY WORDS: · 16S Bacteria Fluorescence FISH Full text pdf format Supplementary material 1 2 PreviousNextCite article as: Apprill A, McNally S, Parsons R, Weber L bacterioplankton. Aquat Microb Ecol 75:129-137. Export citation Tweet linkedIn Cited by Published Vol. 75, No. 2. Online publication date: June 04, 2015 Print ISSN: 0948-3055; 1616-1564 Copyright © Inter-Research.

Язык: Английский

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Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

PLoS ONE, Год журнала: 2014, Номер 9(8), С. e105592 - e105592

Опубликована: Авг. 21, 2014

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification is a critical step. To obtain accurate composition data, must be free bias; however, amplifying all species with equal efficiency from sample containing large variety microorganisms remains challenging. Here, we designed universal primer V3-V4 hypervariable region prokaryotic for simultaneous detection Bacteria Archaea in fecal samples crossbred pigs (Landrace × Large white Duroc) using an Illumina MiSeq next-generation sequencer. In-silico showed that newly primers matched approximately 98.0% 94.6% rRNA gene sequences Ribosomal Database Project database. each sequencing reaction performed primer, average 69,330 (± 20,482) reads were obtained, which archaeal genes comprised 1.2% to 3.2% reads. In addition, frequency belonging phylum Verrucomicrobia, including members classes Verrucomicrobiae Opitutae, was higher NGS than bacterial primer. Importantly, this new set had markedly lower bias most previously primers. Our findings demonstrate present study will permit Archaea, therefore allow more comprehensive understanding structures environmental samples.

Язык: Английский

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The plant microbiome

Genome biology, Год журнала: 2013, Номер 14(6)

Опубликована: Июнь 1, 2013

Plant genomes contribute to the structure and function of plant microbiome, a key determinant health productivity. High-throughput technologies are revealing interactions between these complex communities their hosts in unprecedented detail.

Язык: Английский

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Ecology and exploration of the rare biosphere

Nature Reviews Microbiology, Год журнала: 2015, Номер 13(4), С. 217 - 229

Опубликована: Март 2, 2015

Язык: Английский

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rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

Nucleic Acids Research, Год журнала: 2014, Номер 43(D1), С. D593 - D598

Опубликована: Ноя. 20, 2014

Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys microbial communities. rRNA are often co-located part an rrn operon, and multiple copies this operon present genomes across the tree life. copy number variability provides valuable insight into life history, but introduces systematic bias when measuring community composition surveys. Here we update to database (rrnDB), a publicly available, curated resource for information bacteria archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings substantial increase described, improved curation, mapping both NCBI RDP taxonomies, refined tools querying analyzing these data. With changes, is better positioned remain comprehensive under torrent genome sequencing. enhanced will contribute analysis research linking genomic characteristics history.

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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Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

Nature Biotechnology, Год журнала: 2016, Номер 34(9), С. 942 - 949

Опубликована: Июль 25, 2016

Язык: Английский

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Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

mBio, Год журнала: 2014, Номер 5(4)

Опубликована: Июль 16, 2014

ABSTRACT Microbial communities typically contain many rare taxa that make up the majority of observed membership, yet contribution this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing 3,237 samples from 42 time series nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant brewery wastewater treatment), we introduce a new method detect occasionally become very abundant (conditionally [CRT]) then quantify their contributions temporal shifts in structure. We discovered CRT made 1.5 28% represented broad diversity bacterial archaeal lineages, explained large amounts dissimilarity (i.e., 97% Bray-Curtis dissimilarity). Most were detected at multiple points, though also identified “one-hit wonder” only one point. case study temperate lake, gained additional insights into ecology by comparing routine disturbance events. Our results reveal contribute greater amount than apparent low proportional abundances. This observation was true across wide range ecosystems, indicating these are essential for understanding changes over time. IMPORTANCE processes foundations ecosystems. The ecological roles microorganisms largely unknown, but it thought they stability acting as reservoir can rapidly respond environmental changes. investigated occurrence more prominent (“conditionally rare”). quantified conditionally variety not present all examples, contributed disproportionately when most abundant. result indicates an important general role within communities.

Язык: Английский

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Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats

Scientific Reports, Год журнала: 2015, Номер 5(1)

Опубликована: Сен. 23, 2015

Accumulating evidence suggests that the gut microbiota is an important factor in mediating development of obesity-related metabolic disorders, including type 2 diabetes. Metformin and berberine, two clinically effective drugs for treating diabetes, have recently been shown to exert their actions through modulating microbiota. In this study, we demonstrated metformin berberine similarly shifted overall structure rats. Both showed reverting effects on high-fat diet-induced structural changes The diversity was significantly reduced by both berberine- metformin-treatments. Nearest shrunken centroids analysis identified 134 operational taxonomic units (OTUs) responding treatments, which close associations with obese phenotypes. Sixty out OTUs were decreased drugs, while those belonging putative short-chain fatty acids (SCFA)-producing bacteria, Allobaculum, Bacteriodes, Blautia, Butyricoccus, Phascolarctobacterium, markedly increased and, a lesser extent, metformin. Taken together, our findings suggest similarity microbiota, enrichment SCFA-producing bacteria reduction microbial diversity, may contribute beneficial host.

Язык: Английский

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