Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels

Evaluation of the Use of Formalin-Fixed and Paraffin-Embedded Archive Gastric Tissues for Microbiota Characterization Using Next-Generation Sequencing

(2020) Ines Pinto-Ribeiro et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

(2020) Ching Jian et al.   PLoS One

Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling

(2020) Gabor Fidler et al.   Scientific Reports

Ultrasensitive digital quantification of cytokines and bacteria predicts septic shock outcomes

(2020) M. Fatih Abasıyanık et al.   Nature Communications

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

(2019) Kristýna Fiedorová et al.   Frontiers in Microbiology

Akkermansia muciniphila is a promising probiotic

(2019) Ting Zhang et al.   Microbial Biotechnology

Enrichment of intestinal Lactobacillus by enhanced secretory IgA coating alters glucose homeostasis in P2rx7−/− mice

(2019) Lisa Perruzza et al.   Scientific Reports

Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses

(2019) Francisco Martinez-Hernandez et al.   Frontiers in Microbiology

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

(2019) Lisa Karstens et al.   mSystems

16S rDNA droplet digital PCR for monitoring bacterial DNAemia in bloodstream infections

(2019) Ingrid Ziegler et al.   PLoS One

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

(2019) Petra Videnska et al.   Scientific Reports

Human Endometrial Microbiota at Term of Normal Pregnancies

(2019) Claudia Leoni et al.   Genes

Droplet digital polymerase chain reaction for rapid broad‐spectrum detection of bloodstream infections

(2019) Yannick Wouters et al.   Microbial Biotechnology

Droplet digital PCR quantification of norovirus and adenovirus in decentralized wastewater and graywater collections: Implications for onsite reuse

(2019) Michael A. Jahne et al.   WATER RESEARCH

Comparison between digital PCR and real-time PCR in detection of Salmonella typhimurium in milk

(2018) Meng Wang et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples

(2018) Guillaume Gobert et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

(2018) Henrik Krehenwinkel et al.   PLoS One

Droplet digital polymerase chain reaction (ddPCR) as a novel method for absolute quantification of major gastrointestinal nematodes in sheep

(2018) Safaa T. Elmahalawy et al.   VETERINARY PARASITOLOGY

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

(2018) Francesco Sambo et al.   BMC BIOINFORMATICS

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

High-resolution characterization of the human microbiome

(2017) Cecilia Noecker et al.   Translational Research

T Follicular Helper Cells Promote a Beneficial Gut Ecosystem for Host Metabolic Homeostasis by Sensing Microbiota-Derived Extracellular ATP

(2017) Lisa Perruzza et al.   Cell Reports

Comparison among the Quantification of Bacterial Pathogens by qPCR, dPCR, and Cultural Methods

(2017) Matteo Ricchi et al.   Frontiers in Microbiology

Efficiency and sensitivity of the digital droplet PCR for the quantification of antibiotic resistance genes in soils and organic residues

(2016) Laura Cavé et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Intestinal microbiota sustains inflammation and autoimmunity induced by hypomorphicRAGdefects

(2016) Rosita Rigoni et al.   JOURNAL OF EXPERIMENTAL MEDICINE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Comparison of Droplet Digital PCR and qPCR for the Quantification of Shiga Toxin-Producing Escherichia coli in Bovine Feces

(2016) Bavo Verhaegen et al.   Toxins

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

(2016) Jitendra Kumar et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

(2016) Satyabrata Bag et al.   Scientific Reports

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

(2015) Bruno Fosso et al.   BMC BIOINFORMATICS

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

(2015) Ivan Brukner et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

BALB/c and C57BL/6 Mice Differ in Polyreactive IgA Abundance, which Impacts the Generation of Antigen-Specific IgA and Microbiota Diversity

(2015) Floris Fransen et al.   IMMUNITY

A gut-vascular barrier controls the systemic dissemination of bacteria

(2015) Ilaria Spadoni et al.   SCIENCE

Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot

(2014) Tanja Dreo et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

(2014) Caterina Manzari et al.   BIOLOGICAL INVASIONS

A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2

(2014) Marc A. Sze et al.   PLoS One

Further Steps in TANGO: improved taxonomic assignment in metagenomics

(2013) D. Alonso-Alemany et al.   BIOINFORMATICS

Absolute quantification by droplet digital PCR versus analog real-time PCR

(2013) Christopher M Hindson et al.   NATURE METHODS

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

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Evaluation of a Droplet Digital Polymerase Chain Reaction Format for DNA Copy Number Quantification

(2011) Leonardo B. Pinheiro et al.   ANALYTICAL CHEMISTRY

Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

(2010) Bärbel Stecher et al.   PLoS Pathogens

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH