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Toward standards in clinical microbiome studies: comparison of three DNA extraction methods and two bioinformatic pipelines

https://doi.org/10.1101/751123
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What this work says

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

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ggplot2: Elegant Graphics for Data Analysis
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Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms
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Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment
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Clostridioides difficile contamination in a clinical microbiology laboratory?
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Review of squamous premalignant vulvar lesions
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Reply to Meisel et al.
inferredcites →https://doi.org/10.1016/j.tim.2018.11.003openalex-snapshot
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
inferredcites →https://doi.org/10.1016/j.transproceed.2017.12.043openalex-snapshot
Council of Europe Black Sea Area Project: International Cooperation for the Development of Activities Related to Donation and Transplantation of Organs in the Region
inferredcites →https://doi.org/10.1016/s0140-6736(03)12489-0openalex-snapshot
Gut flora in health and disease
inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot
A human gut microbial gene catalogue established by metagenomic sequencing
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nbt.3960openalex-snapshot
Towards standards for human fecal sample processing in metagenomic studies
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.2276openalex-snapshot
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
inferredcites →https://doi.org/10.1038/nrg3129openalex-snapshot
Experimental and analytical tools for studying the human microbiome
inferredcites →https://doi.org/10.1038/s41579-018-0089-xopenalex-snapshot
The oral microbiota: dynamic communities and host interactions
inferredcites →https://doi.org/10.1038/s41585-018-0104-zopenalex-snapshot
Community profiling of the urinary microbiota: considerations for low-biomass samples
inferredcites →https://doi.org/10.1038/s41586-019-1451-5openalex-snapshot
Human placenta has no microbiome but can contain potential pathogens
inferredcites →https://doi.org/10.1038/s41598-017-07885-3openalex-snapshot
The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
inferredcites →https://doi.org/10.1038/s41598-018-29054-wopenalex-snapshot
The urinary microbiome associated with bladder cancer
inferredcites →https://doi.org/10.1038/srep26276openalex-snapshot
RETRACTED ARTICLE: Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies
inferredcites →https://doi.org/10.1038/srep45536openalex-snapshot
Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling
inferredcites →https://doi.org/10.1053/j.gastro.2018.04.028openalex-snapshot
Association Between Bacteremia From Specific Microbes and Subsequent Diagnosis of Colorectal Cancer
inferredcites →https://doi.org/10.1080/14712598.2018.1542426openalex-snapshot
The immune microenvironment in vulvar (pre)cancer: review of literature and implications for immunotherapy
inferredcites →https://doi.org/10.1093/femsec/fiz045openalex-snapshot
Issues and current standards of controls in microbiome research
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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/10.1111/j.1462-2920.2007.01369.xopenalex-snapshot
Diversity of the human gastrointestinal tract microbiota revisited
inferredcites →https://doi.org/10.1128/aem.01282-13openalex-snapshot
Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity
inferredcites →https://doi.org/10.1128/jcm.02876-13openalex-snapshot
Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder
inferredcites →https://doi.org/10.1128/jcm.05852-11openalex-snapshot
Evidence of Uncultivated Bacteria in the Adult Female Bladder
inferredcites →https://doi.org/10.1128/jcm.43.11.5721-5732.2005openalex-snapshot
Defining the Normal Bacterial Flora of the Oral Cavity
inferredcites →https://doi.org/10.1128/msystems.00186-19openalex-snapshot
Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
inferredcites →https://doi.org/10.1136/gutjnl-2018-317200openalex-snapshot
Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin
inferredcites →https://doi.org/10.1158/2159-8290.cd-17-1134openalex-snapshot
The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression
inferredcites →https://doi.org/10.1186/1471-2180-14-112openalex-snapshot
Processing faecal samples: a step forward for standards in microbial community analysis
inferredcites →https://doi.org/10.1186/s12864-018-4703-0openalex-snapshot
Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
inferredcites →https://doi.org/10.1186/s12866-019-1391-0openalex-snapshot
Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI
inferredcites →https://doi.org/10.1186/s12915-014-0087-zopenalex-snapshot
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
inferredcites →https://doi.org/10.1186/s13073-016-0307-yopenalex-snapshot
The healthy human microbiome
inferredcites →https://doi.org/10.1186/s40168-015-0087-4openalex-snapshot
16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
inferredcites →https://doi.org/10.1186/s40168-016-0172-3openalex-snapshot
Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota
inferredcites →https://doi.org/10.1186/s40168-017-0396-xopenalex-snapshot
Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling
inferredcites →https://doi.org/10.1214/aoms/1177729694openalex-snapshot
On Information and Sufficiency
inferredcites →https://doi.org/10.12688/f1000research.9227.2openalex-snapshot
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.1371/journal.pone.0088982openalex-snapshot
The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0119355openalex-snapshot
The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations
inferredcites →https://doi.org/10.1371/journal.pone.0169877openalex-snapshot
Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.3389/fmicb.2016.00459openalex-snapshot
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
inferredcites →https://doi.org/10.7287/peerj.preprints.27295v1openalex-snapshot
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

What points at this work

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

inferred← citeshttps://doi.org/10.3390/genes11091015openalex-snapshot
Challenges in Human Skin Microbial Profiling for Forensic Science: A Review
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