DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, Journal Year: 2016, Volume and Issue: 13(7), P. 581 - 583

Published: May 23, 2016

Language: Английский

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Ribosomal Database Project: data and tools for high throughput rRNA analysis

Nucleic Acids Research, Journal Year: 2013, Volume and Issue: 42(D1), P. D633 - D642

Published: Nov. 27, 2013

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along tools to allow researchers analyze their own sequences in RDP framework. data are utilized fields as diverse human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy phylogenetics. In addition collections of bacterial archaeal small subunit genes, now includes a collection fungal large genes. tools, including Classifier Aligner, have been updated work this new collection. The use high-throughput sequencing characterize populations has exploded past several years, technologies improved, sizes datasets increased. With release 11, is providing an expanded set facilitate analysis both single-stranded paired-end reads. addition, most available open source packages for download local by high-volume needs or who would like develop custom pipelines.

Language: Английский

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Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

Environmental Microbiology, Journal Year: 2015, Volume and Issue: 18(5), P. 1403 - 1414

Published: Aug. 14, 2015

Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated Gammaproteobacteria) common marine taxa. evaluated samples mock communities (containing 11 27 clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, amplify eukaryotic 18S rRNA. Mock 515F-Y/926R yielded closer observed composition versus expected (r(2) = 0.95) compared 515F-Y/806R ∼ 0.5). Unexpectedly, biases against SAR11 in field (∼4-10-fold) were stronger than (∼2-fold). Correcting a mismatch to Thaumarchaea 515F-C increased their apparent abundance samples, but not as much using rather 806R. With plankton rich DNA (> 1 μm size fraction), sequences averaged ∼17% all sequences. A single strongly bias amplification, even perfectly matched exhibit preferential amplification. show beyond silico predictions, testing important selection.

Language: Английский

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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

BMC Biology, Journal Year: 2014, Volume and Issue: 12(1)

Published: Nov. 12, 2014

The study of microbial communities has been revolutionised in recent years by the widespread adoption culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder these sequence-based approaches is presence contamination DNA extraction kits other laboratory reagents. In this we demonstrate that contaminating ubiquitous commonly used reagents, varies greatly composition between different kit batches, critically impacts results obtained from samples containing a low biomass. Contamination both PCR-based surveys shotgun We provide an extensive list genera, guidelines on how to mitigate effects contamination. These suggest caution should be advised when applying microbiota present biomass environments. Concurrent negative control strongly advised.

Language: Английский

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Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(12), P. 2639 - 2643

Published: July 21, 2017

Abstract Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting the customary construction of molecular operational taxonomic units (OTUs): clusters reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such amplicon sequence variants (ASVs) can be resolved exactly, down level single-nucleotide differences over sequenced gene region. The benefits finer resolution are immediately apparent, and arguments for ASV focused on their improved resolution. Less obvious, but we believe more important, broad derive from status ASVs as consistent labels with intrinsic biological meaning identified independently reference database. Here discuss how these features grant combined advantages closed-reference OTUs—including computational costs scale linearly study size, simple merging between processed sets, forward prediction—and de novo accurate measurement diversity applicability communities lacking deep coverage in databases. We argue improvements reusability, reproducibility comprehensiveness great should replace OTUs standard unit analysis reporting.

Language: Английский

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A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

Cell, Journal Year: 2016, Volume and Issue: 167(5), P. 1339 - 1353.e21

Published: Nov. 1, 2016

Language: Английский

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

Aquatic Microbial Ecology, Journal Year: 2015, Volume and Issue: 75(2), P. 129 - 137

Published: April 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.

Language: Английский

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Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

mSystems, Journal Year: 2015, Volume and Issue: 1(1)

Published: Dec. 18, 2015

Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is difficult challenge, and the comparability data sets amplified with requires attention. Here, we examined performance modified 16S rRNA gene internal transcribed spacer (ITS) archaea/bacteria fungi, respectively, nonaquatic samples. We moved primer bar codes to 5' end, allowing different 3' pairings, such as 515f/926r pair, which amplifies variable regions 4 5 gene. additionally demonstrated modifications 515f/806r (variable region 4) improves detection Thaumarchaeota clade SAR11 marine samples, do not degrade on taxa already effectively by original set. Alterations fungal ITS did result differential but overall improved compared primers. In both cases, should be widely adopted amplicon studies. IMPORTANCE continue uncover wealth information connecting microbes important ways human environmental ecology. As our scientific knowledge technical abilities improve, tools used microbiome can improve accuracy techniques, ensuring identify groundbreaking connections between ecosystems they populate, from ice caps body. It confirm these cause new, detrimental biases would inhibit field rather than move it forward. therefore two recently pairs target taxonomically discriminatory bacterial genomic DNA introduce new when variety sample types, soil skin. This confirms utility maintaining currently recommended research techniques state art.

Language: Английский

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Human gut microbes impact host serum metabolome and insulin sensitivity

Nature, Journal Year: 2016, Volume and Issue: 535(7612), P. 376 - 381

Published: July 1, 2016

Language: Английский

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Gut microbiome alterations in Alzheimer’s disease

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Oct. 13, 2017

Alzheimer's disease (AD) is the most common form of dementia. However, etiopathogenesis this devastating not fully understood. Recent studies in rodents suggest that alterations gut microbiome may contribute to amyloid deposition, yet microbial communities associated with AD have been characterized humans. Towards end, we bacterial taxonomic composition fecal samples from participants and without a diagnosis dementia due AD. Our analyses revealed has decreased diversity compositionally distinct control age- sex-matched individuals. We identified phylum- through genus-wide differences abundance including Firmicutes, increased Bacteroidetes, Bifidobacterium participants. Furthermore, observed correlations between levels differentially abundant genera cerebrospinal fluid (CSF) biomarkers These findings add growing list diseases alterations, as well be target for therapeutic intervention.

Language: Английский

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