Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

PubWeight™: 12.26‹?› | Rank: Top 0.1% | All-Time Top 10000

🔗 View Article (PMC 3237409)

Published in PLoS One on December 14, 2011

Authors

Patrick D Schloss1, Dirk Gevers, Sarah L Westcott

Author Affiliations

1: Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America. pschloss@umich.edu

Articles citing this

(truncated to the top 100)

UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods (2013) 12.05

A framework for human microbiome research. Nature (2012) 11.41

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res (2012) 6.21

Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39

A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One (2012) 4.35

Inferring correlation networks from genomic survey data. PLoS Comput Biol (2012) 3.80

Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med (2013) 3.65

Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One (2012) 3.49

Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30

Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med (2015) 2.97

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J (2013) 2.90

Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis (2012) 2.72

The gut microbiome modulates colon tumorigenesis. MBio (2013) 2.45

Dynamics and associations of microbial community types across the human body. Nature (2014) 2.32

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One (2012) 2.31

The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J (2012) 2.13

Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc (2013) 2.05

Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees. PLoS One (2012) 2.04

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood (2014) 2.04

Genomic approaches to studying the human microbiota. Nature (2012) 2.00

Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res (2013) 1.78

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One (2012) 1.77

Gut microbiome-derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease. Nat Immunol (2016) 1.75

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat Commun (2015) 1.68

The human microbiome: our second genome. Annu Rev Genomics Hum Genet (2012) 1.64

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol (2013) 1.62

Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio (2015) 1.56

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome (2013) 1.55

The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One (2012) 1.50

Microbiome profiles in periodontitis in relation to host and disease characteristics. PLoS One (2015) 1.50

Stabilization of the murine gut microbiome following weaning. Gut Microbes (2012) 1.49

Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PLoS One (2012) 1.49

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One (2015) 1.45

High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl Environ Microbiol (2012) 1.43

Microbial stimulation and succession following a test well injection simulating CO2 leakage into a shallow newark basin aquifer. PLoS One (2015) 1.41

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets. PLoS One (2016) 1.40

Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany. PLoS One (2015) 1.40

Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. MBio (2014) 1.40

Analysis of the duodenal microbiotas of weaned piglet fed with epidermal growth factor-expressed Saccharomyces cerevisiae. BMC Microbiol (2016) 1.39

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS One (2012) 1.35

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol Lett (2014) 1.33

Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species. PLoS One (2013) 1.31

Using high throughput sequencing to explore the biodiversity in oral bacterial communities. Mol Oral Microbiol (2012) 1.30

CREST--classification resources for environmental sequence tags. PLoS One (2012) 1.28

Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One (2013) 1.27

Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A (2013) 1.27

Distribution-based clustering: using ecology to refine the operational taxonomic unit. Appl Environ Microbiol (2013) 1.25

Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J (2012) 1.24

Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov (2015) 1.23

Library construction for next-generation sequencing: overviews and challenges. Biotechniques (2014) 1.20

The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl Environ Microbiol (2014) 1.19

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J (2014) 1.19

Intestinal Blautia Is Associated with Reduced Death from Graft-versus-Host Disease. Biol Blood Marrow Transplant (2015) 1.19

Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. Eur J Clin Microbiol Infect Dis (2013) 1.19

Bacterial community development in experimental gingivitis. PLoS One (2013) 1.19

Alterations in the colonic microbiota in response to osmotic diarrhea. PLoS One (2013) 1.16

Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci (2014) 1.15

Comparison of storage conditions for human vaginal microbiome studies. PLoS One (2012) 1.14

Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium difficile infection. Antimicrob Agents Chemother (2014) 1.14

Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One (2013) 1.14

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet. ISME J (2014) 1.13

Intestinal microbiota composition of interleukin-10 deficient C57BL/6J mice and susceptibility to Helicobacter hepaticus-induced colitis. PLoS One (2013) 1.12

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol (2013) 1.12

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland. ISME J (2012) 1.12

Bacterial taxa-area and distance-decay relationships in marine environments. Mol Ecol (2014) 1.11

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio (2015) 1.09

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units. PeerJ (2015) 1.08

A direct PCR approach to accelerate analyses of human-associated microbial communities. PLoS One (2012) 1.08

Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems. PLoS One (2015) 1.08

Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges. ISME J (2015) 1.07

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J (2014) 1.06

Coal-packed methane biofilter for mitigation of green house gas emissions from coal mine ventilation air. PLoS One (2014) 1.06

454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One (2013) 1.05

The dynamics of a family's gut microbiota reveal variations on a theme. Microbiome (2014) 1.05

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ (2016) 1.04

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians. ISME J (2013) 1.04

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol (2013) 1.04

New perspectives on viable microbial communities in low-biomass cleanroom environments. ISME J (2012) 1.03

Metagenomics for pathogen detection in public health. Genome Med (2013) 1.03

Bacterial communities associated with surfaces of leafy greens: shift in composition and decrease in richness over time. Appl Environ Microbiol (2014) 1.03

Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections. J Clin Microbiol (2014) 1.02

Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytol (2014) 1.02

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med (2015) 1.01

Clinical microbiology informatics. Clin Microbiol Rev (2014) 1.01

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J (2012) 1.00

Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PLoS One (2012) 0.99

Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med (2016) 0.99

High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism. Bioinform Biol Insights (2014) 0.99

Improved inference of taxonomic richness from environmental DNA. PLoS One (2013) 0.99

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny. ISME J (2013) 0.99

Small changes in pH have direct effects on marine bacterial community composition: a microcosm approach. PLoS One (2012) 0.99

Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times. PLoS One (2014) 0.99

Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform (2013) 0.98

Assessing the consequences of denoising marker-based metagenomic data. PLoS One (2013) 0.98

Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan. Sci Rep (2014) 0.98

Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiol (2012) 0.97

Articles cited by this

Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38

UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22

The human microbiome project. Nature (2007) 28.53

The NIH Human Microbiome Project. Genome Res (2009) 24.61

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67

Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64

Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol (1996) 20.84

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (2004) 18.87

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21

At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol (2005) 15.41

Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25

Microbial population structures in the deep marine biosphere. Science (2007) 14.61

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17

Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45

Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol (2010) 13.19

The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99

Identification of the uncultured bacillus of Whipple's disease. N Engl J Med (1992) 12.33

Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82

Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol (1998) 10.53

DNA sequence quality trimming and vector removal. Bioinformatics (2001) 10.04

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18

Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev (1996) 6.12

Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res (2002) 6.07

PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res (1996) 6.04

PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol (2005) 5.97

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol (2008) 4.58

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol (2011) 4.55

Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol (1999) 4.53

Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol (1997) 3.78

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol (2010) 3.26

A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One (2009) 3.07

Replicate or lie. Environ Microbiol (2010) 2.09

[Fecal dysbiosis in infancy]. Z Kinderheilkd (1959) 1.06

Articles by these authors

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21

Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53

A catalog of reference genomes from the human microbiome. Science (2010) 8.10

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53

Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res (2011) 5.97

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41

Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol (2012) 5.35

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol (2011) 4.55

Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science (2008) 3.46

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med (2013) 3.39

Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol (2012) 3.02

Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol (2009) 2.61

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin Infect Dis (2014) 2.41

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest (2014) 2.39

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J (2012) 2.13

Structural basis of DNA replication origin recognition by an ORC protein. Science (2007) 2.00

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One (2012) 1.98

The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe (2011) 1.97

Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev (2005) 1.87

Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio (2012) 1.85

High-quality draft genome sequences of 28 Enterococcus sp. isolates. J Bacteriol (2010) 1.67

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One (2012) 1.66

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome (2013) 1.58

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology (2005) 1.49

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol (2007) 1.45

Conservation of the chitin utilization pathway in the Vibrionaceae. Appl Environ Microbiol (2007) 1.40

Exploring physical therapy clinical decision making for children with spastic diplegia: survey of pediatric practice. Pediatr Phys Ther (2005) 1.39

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol (2012) 1.35

The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol (2006) 1.33

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics (2008) 1.32

Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet (2011) 1.30

Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol (2007) 1.30

Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix. J Mol Biol (2006) 1.16

Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats. FEMS Microbiol Ecol (2006) 1.08

Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. J Innate Immun (2013) 1.02

Identification of Bifidobacterium species using rep-PCR fingerprinting. Syst Appl Microbiol (2003) 0.99

Vibrio chromosomes share common history. BMC Microbiol (2010) 0.95

MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res (2013) 0.93

Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis. Inflamm Bowel Dis (2010) 0.92

Timed up and down stairs test: preliminary reliability and validity of a new measure of functional mobility. Pediatr Phys Ther (2004) 0.90

Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir) gene phylogeny in cultivated denitrifiers. Environ Microbiol (2007) 0.89

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease. Inflamm Bowel Dis (2016) 0.87

Responsiveness of the Test of Infant Motor Performance (TIMP) in infants born preterm. Pediatr Phys Ther (2005) 0.84

Muscle force and range of motion as predictors of standing balance in children with cerebral palsy. Phys Occup Ther Pediatr (2004) 0.83

Biphasic kinetics of growth and bacteriocin production with Lactobacillus amylovorus DCE 471 occur under stress conditions. Microbiology (2003) 0.83

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell (2016) 0.82

Genomic and phenotypic comparison of Bacillus fumarioli isolates from geothermal Antarctic soil and gelatine. Res Microbiol (2004) 0.81

Physical therapy clinical management recommendations for children with cerebral palsy - spastic diplegia: achieving functional mobility outcomes. Pediatr Phys Ther (2006) 0.78

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest (2015) 0.77

Dirk Gevers. Nat Rev Drug Discov (2015) 0.75

Synthesis and luminescence of ZnMgS:Mn2+ nanoparticles. J Nanosci Nanotechnol (2005) 0.75