Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

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

Опубликована: Май 17, 2018

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. evaluated optimized commonly used implemented 1 (RDP, BLAST, UCLUST, SortMeRNA) new (a scikit-learn naive Bayes classifier, consensus based on VSEARCH, BLAST+) bacterial 16S rRNA fungal ITS amplicon sequence data. The naive-Bayes, BLAST+-based, VSEARCH-based classifiers meet or exceed the species-level accuracy other designed marker gene that were this work. These evaluations, 19 mock communities error-free simulations, including simulated "novel" sequences, are available our extensible benchmarking framework, tax-credit https://github.com/caporaso-lab/tax-credit-data ). Our results illustrate importance parameter tuning optimizing classifier performance, we make recommendations regarding choices these under range standard operating conditions. both free, open-source, BSD-licensed packages GitHub.

Язык: Английский

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Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

Science, Год журнала: 2017, Номер 359(6371), С. 97 - 103

Опубликована: Ноя. 2, 2017

Preclinical mouse models suggest that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy; however, this has not been well-characterized in human cancer patients. Here we examined oral and of melanoma patients undergoing anti-programmed cell death 1 protein (PD-1) immunotherapy (

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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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

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

Опубликована: Март 8, 2017

High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding complex microbial communities, but the inherent noise in PCR and DNA limits differentiation closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq HiSeq platforms. Deblur substantially reduces computational demands relative similar sOTU methods does so or better sensitivity Using simulations, mock mixtures, real data sets, detected bacterial single nucleotide differences while removing false positives maintaining stability detection, suggesting is limited only by read length diversity within amplicon sequences. Because operates on per-sample level, it scales modern sets meta-analyses. To highlight Deblur's ability integrate include an interactive exploration its application multiple distinct rounds American Gut Project. open source under Berkeley Software Distribution (BSD) license, easily installable, downloadable https://github.com/biocore/deblur. IMPORTANCE provides rapid sensitive means assess patterns driven taxa. This algorithm solution problem identifying between taxa whose differ base pair, applicable automated fashion large-scale runs collected over time.

Язык: Английский

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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Molecular Ecology, Год журнала: 2017, Номер 26(21), С. 5872 - 5895

Опубликована: Сен. 18, 2017

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid of DNA from diverse kinds environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences eDNA a taxonomic name is called "eDNA metabarcoding" and offers powerful molecular tool capable noninvasively surveying species richness many ecosystems. Here, review use metabarcoding for animal plant richness, challenges in using approaches estimate relative abundance. We highlight applications freshwater, marine terrestrial environments, this broad context, distill what known about different sample types approximate space across time. provide guiding questions study design discuss workflow focus primers library preparation methods. additionally important criteria consideration bioinformatic filtering data sets, recommendations increasing transparency. Finally, looking future, emerging ecology, conservation, invasion biology, biomonitoring, can empower citizen science education.

Язык: Английский

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Soil bacterial networks are less stable under drought than fungal networks

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Июль 27, 2018

Abstract Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown how co-occurrence networks within these respond to disturbances such as climate extremes. This represents an important knowledge gap because changes could have implications for their functioning and vulnerability future disturbances. Here, we show grassland mesocosms that drought promotes destabilising properties soil bacterial, not fungal, networks, bacterial link more strongly during recovery than do fungal communities. Moreover, reveal has prolonged effect on via vegetation composition resultant reductions moisture. Our results provide new insight the mechanisms through which alters with potential long-term consequences, including plant community ability of aboveground belowground withstand

Язык: Английский

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ASAP: assemble species by automatic partitioning

Molecular Ecology Resources, Год журнала: 2020, Номер 21(2), С. 609 - 620

Опубликована: Окт. 15, 2020

Abstract Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough split sets as large 10 4 sequences into putative in several minutes. Although grounded evolutionary theory, the implementation of hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding computational burden phylogenetic reconstruction. Importantly, proposes ranked scoring system no biological prior insight intraspecific diversity. stand‐alone program can be used either through graphical web‐interface or downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP GMYC) on real COI representing various degrees challenge (from small easy cases complicated also Monte‐Carlo simulations multispecies coalescent framework assess strengths weaknesses other programs. Through these analyses, demonstrate has potential become major tool taxonomists it rapidly full exploratory interface relevant hypothesis first step integrative taxonomy process.

Язык: Английский

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Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Cell, Год журнала: 2019, Номер 177(6), С. 1600 - 1618.e17

Опубликована: Май 1, 2019

Язык: Английский

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Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Science, Год журнала: 2019, Номер 366(6465), С. 606 - 612

Опубликована: Окт. 31, 2019

Protecting plants from the inside out Some soils show a remarkable ability to suppress disease caused by plant pathogens, an that is attributed plant-associated microbiota. Carrión et al. investigated role of endophytes, intimate microbial community found within roots, in fungal suppression (see Perspective Tringe). The wilt fungus Rhizoctonia solani infects sugar beets, whereupon transcriptional analysis shows several bacterial endophyte species activate biosynthetic gene clusters cause suppression. These organisms produce antifungal effectors, including enzymes can digest cell walls, and secondary metabolites, phenazines, polyketides, siderophores, which may contribute phenotype. Science , this issue p. 606 ; see also 568

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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