Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies

Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

(2021) Eduard Fadeev et al.   Frontiers in Microbiology

Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

(2021) Janneke Schreuder et al.   Frontiers in Microbiology

Feeding dairy cows bakery by-products enhanced nutrient digestibility, but affected fecal microbial composition and pH in a dose-dependent manner

(2021) A. Kaltenegger et al.   JOURNAL OF DAIRY SCIENCE

Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

(2021) Patrick D. Schloss   mSphere

DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

(2021) Erika Ganda et al.   mSystems

powmic: an R package for power assessment in microbiome case–control studies

(2020) Li Chen   BIOINFORMATICS

Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

(2020) Shantelle Claassen-Weitz et al.   BMC MICROBIOLOGY

The day‐to‐day stability of the ruminal and fecal microbiota in lactating dairy cows

(2020) Shuai Huang et al.   MicrobiologyOpen

A reasonable correlation between cloacal and cecal microbiomes in broiler chickens

(2020) Nadia A. Andreani et al.   POULTRY SCIENCE

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

(2020) Viktoria Neubauer et al.   Animals

Effects of Chemical and Mechanical Lysis on Microbial DNA Yield, Integrity, and Downstream Amplicon Sequencing of Rumen Bacteria and Protozoa

(2020) Zhi Yuan Ma et al.   Frontiers in Microbiology

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater

(2019) Julien Tap et al.   Scientific Reports

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics

(2019) Katherine L. Huebner et al.   Scientific Reports

Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study

(2019) Shirin Moossavi et al.   BMC MICROBIOLOGY

Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

(2019) Lisa Karstens et al.   mSystems

Ecology of Subseafloor Crustal Biofilms

(2019) Gustavo A. Ramírez et al.   Frontiers in Microbiology

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum

(2019) Michael J. Rothrock et al.   Frontiers in Veterinary Science

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids

(2019) Roland Martzy et al.   Scientific Reports

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity

(2019) Lauren V. Carruthers et al.   PeerJ

Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract

(2018) Simon Graspeuntner et al.   Scientific Reports

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms

(2018) John A. Handley et al.   Frontiers in Microbiology

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi

(2018) Zhuoran Han et al.   MicrobiologyOpen

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

(2018) Nicholas A. Bokulich et al.   Microbiome

“Available upon request”: not good enough for microbiome data!

(2018) Morgan G. I. Langille et al.   Microbiome

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?

(2018) Tansol Park et al.   Frontiers in Microbiology

Uterine microbiome—low biomass and high expectations†

(2018) Iolanda Garcia-Grau et al.   BIOLOGY OF REPRODUCTION

The majority is uncultured

(2018) Ursula Hofer   NATURE REVIEWS MICROBIOLOGY

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

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

(2017) Benjamin J Callahan et al.   ISME Journal

Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this affect sampling strategies for whole-house microbiomic studies?

(2017) Aude Locatelli et al.   JOURNAL OF APPLIED POULTRY RESEARCH

Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge

(2017) Jan C. Plaizier et al.   MICROBIAL ECOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

A Review on Macroscale and Microscale Cell Lysis Methods

(2017) Mohammed Shehadul Islam et al.   Micromachines

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach

(2017) Sun Ae Kim et al.   Scientific Reports

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design

(2016) Jacquelyn S. Meisel et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

The bovine milk microbiota: insights and perspectives from -omics studies

(2016) M. F. Addis et al.   Molecular BioSystems

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Assessing the microbiomes of scalder and chiller tank waters throughout a typical commercial poultry processing day

(2016) M. J. Rothrock et al.   POULTRY SCIENCE

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota

(2016) Christina Gill et al.   PLoS One

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

(2015) Brendan J. Kelly et al.   BIOINFORMATICS

Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences

(2015) Dragana Stanley et al.   BMC MICROBIOLOGY

Exploring deep microbial life in coal-bearing sediment down to  2.5 km below the ocean floor

(2015) F. Inagaki et al.   SCIENCE

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Microbiota of the indoor environment: a meta-analysis

(2015) Rachel I. Adams et al.   Microbiome

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Context and the human microbiome

(2015) Daniel McDonald et al.   Microbiome

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

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

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

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

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

(2012) Feng Guo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characterization of Effect of Repeated Freeze and Thaw Cycles on Stability of Genomic DNA Using Pulsed Field Gel Electrophoresis

(2012) Wen Shao et al.   BIOPRESERVATION AND BIOBANKING

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A Format for Phylogenetic Placements

(2012) Frederick A. Matsen et al.   PLoS One

The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples

(2011) Johanna Maukonen et al.   FEMS MICROBIOLOGY ECOLOGY

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment

(2011) Jessica L. Danzeisen et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Negative Controls

(2010) Marc Lipsitch et al.   EPIDEMIOLOGY

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

(2010) Anne Salonen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Dietary Interactions and Interventions Affecting Escherichia coli O157 Colonization and Shedding in Cattle

(2009) Megan E. Jacob et al.   Foodborne Pathogens and Disease

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

(2008) Ani Qu et al.   PLoS One