Similarity in milk microbiota in replicates

The Effects of High Fiber Rye, Compared to Refined Wheat, on Gut Microbiota Composition, Plasma Short Chain Fatty Acids, and Implications for Weight Loss and Metabolic Risk Factors (the RyeWeight Study)

(2022) Kia Nøhr Iversen et al.   Nutrients

Bovine milk microbiota: Evaluation of different DNA extraction protocols for challenging samples

(2022) Julia A. Schwenker et al.   MicrobiologyOpen

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota

(2021) Shirin Moossavi et al.   Microbiome

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

(2021) Denise M. O’Sullivan et al.   Scientific Reports

Identifying biases and their potential solutions in human microbiome studies

(2021) Jacob T. Nearing et al.   Microbiome

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary

(2019) Clarisse Marotz et al.   BIOTECHNIQUES

Distribution of bacteria between different milk fractions, investigated using culture‐dependent methods and molecular‐based and fluorescent microscopy approaches

(2019) L. Sun et al.   JOURNAL OF APPLIED MICROBIOLOGY

Human placenta has no microbiome but can contain potential pathogens

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

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

(2019) Josef Dahlberg et al.   PLoS One

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

(2019) Lisa Karstens et al.   mSystems

Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows

(2018) Svetlana Ferreira Lima et al.   PLoS One

The distribution of bacterial doubling times in the wild

(2018) Beth Gibson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Effect of Lipopolysaccharide-Induced Experimental Bovine Mastitis on Clinical Parameters, Inflammatory Markers, and the Metabolome: A Kinetic Approach

(2018) Carl-Fredrik Johnzon et al.   Frontiers in Immunology

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The composition of the perinatal intestinal microbiota in cattle

(2018) Mohammad Jaber Alipour et al.   Scientific Reports

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

(2018) Nicole M. Davis et al.   Microbiome

The structured diversity of specialized gut symbionts of the New World army ants

(2017) Piotr Łukasik et al.   MOLECULAR ECOLOGY

Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines

(2017) Erika K. Ganda et al.   Microbiome

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

(2017) Chongqing Wen et al.   PLoS One

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

(2014) Luisa W. Hugerth et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH