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Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/mbo3.453openalex-snapshot

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis

inferredcites →https://doi.org/10.1007/978-1-4939-3185-9_4openalex-snapshot

Techniques for Nucleic Acid Purification from Plant, Animal, and Microbial Samples

inferredcites →https://doi.org/10.1007/s00253-012-4244-4openalex-snapshot

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

inferredcites →https://doi.org/10.1016/j.chom.2016.12.014openalex-snapshot

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome

inferredcites →https://doi.org/10.1016/j.mimet.2007.11.007openalex-snapshot

Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces

inferredcites →https://doi.org/10.1038/ismej.2014.117openalex-snapshot

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

inferredcites →https://doi.org/10.1038/ismej.2014.195openalex-snapshot

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ismej.2017.4openalex-snapshot

Annual community patterns are driven by seasonal switching between closely related marine bacteria

inferredcites →https://doi.org/10.1038/nature23889openalex-snapshot

Strains, functions and dynamics in the expanded Human Microbiome Project

inferredcites →https://doi.org/10.1038/nbt.3981openalex-snapshot

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

inferredcites →https://doi.org/10.1038/nmeth.1184openalex-snapshot

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot

QIIME allows analysis of high-throughput community sequencing data

inferredcites →https://doi.org/10.1038/npjbiofilms.2016.4openalex-snapshot

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

inferredcites →https://doi.org/10.1038/srep40579openalex-snapshot

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

inferredcites →https://doi.org/10.1073/pnas.0409727102openalex-snapshot

Genomic insights that advance the species definition for prokaryotes

inferredcites →https://doi.org/10.1073/pnas.1000080107openalex-snapshot

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot

Search and clustering orders of magnitude faster than BLAST

inferredcites →https://doi.org/10.1093/femsle/fnx092openalex-snapshot

Soil microbiome transfer method affects microbiome composition, including dominant microorganisms, in a novel environment

inferredcites →https://doi.org/10.1093/nar/gku1341openalex-snapshot

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

inferredcites →https://doi.org/10.1101/081257openalex-snapshot

UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

inferredcites →https://doi.org/10.1101/gr.151803.112openalex-snapshot

Meta-analyses of studies of the human microbiota

inferredcites →https://doi.org/10.1111/1574-6941.12219openalex-snapshot

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

inferredcites →https://doi.org/10.1111/2041-210x.12114openalex-snapshot

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

inferredcites →https://doi.org/10.1111/gcb.13557openalex-snapshot

Identifying the microbial taxa that consistently respond to soil warming across time and space

inferredcites →https://doi.org/10.1111/j.1574-6968.2012.02523.xopenalex-snapshot

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

inferredcites →https://doi.org/10.1128/aem.02810-10openalex-snapshot

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

inferredcites →https://doi.org/10.1128/mbio.00836-16openalex-snapshot

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

inferredcites →https://doi.org/10.1128/msystems.00003-15openalex-snapshot

Open-Source Sequence Clustering Methods Improve the State Of the Art

inferredcites →https://doi.org/10.1128/msystems.00191-16openalex-snapshot

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

inferredcites →https://doi.org/10.1177/1040638712466395openalex-snapshot

Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis by polymerase chain reaction

inferredcites →https://doi.org/10.1186/1471-2105-13-283openalex-snapshot

Denoising PCR-amplified metagenome data

inferredcites →https://doi.org/10.1186/gb-2011-12-2-r18openalex-snapshot

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

inferredcites →https://doi.org/10.1186/gb-2011-12-6-r60openalex-snapshot

Metagenomic biomarker discovery and explanation

inferredcites →https://doi.org/10.1371/journal.pone.0032118openalex-snapshot

Analyses of the Microbial Diversity across the Human Microbiome

inferredcites →https://doi.org/10.3354/ame033107openalex-snapshot

Recolonization and cues for bacterial migration into 'mock' deposit-feeder fecal casts

inferredcites →https://doi.org/10.3945/ajcn.115.126375openalex-snapshot

Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome

inferredcites →https://doi.org/10.3945/jn.116.238816openalex-snapshot

Early-Life Sugar Consumption Affects the Rat Microbiome Independently of Obesity

inferredcites →https://doi.org/10.7717/peerj.1702openalex-snapshot

Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice

inferredcites →https://doi.org/10.7717/peerj.3889openalex-snapshot

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/aps3.11444openalex-snapshot

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

inferred← citeshttps://doi.org/10.1002/edn3.44openalex-snapshot

Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water

inferred← citeshttps://doi.org/10.1093/advances/nmz022openalex-snapshot

The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models—Part I: Overview of Current Methods

inferred← citeshttps://doi.org/10.1101/429993openalex-snapshot

Evaluating intraspecific genetic diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences

inferred← citeshttps://doi.org/10.29328/journal.abse.1001011openalex-snapshot

Fecal storage condition induces variations of microbial composition and differential interpretation of metagenomic analysis

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