Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss

(2018) O. Gonzalez-Recio et al.   JOURNAL OF DAIRY SCIENCE

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria

(2018) Mohamed K. Abdelmegeid et al.   Journal of Animal Science and Biotechnology

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

(2018) Jinjin Tong et al.   PLoS One

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate

(2017) Milka Popova et al.   Frontiers in Microbiology

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Short communication: The effect of an exogenous enzyme with amylolytic activity on gas production and in vitro rumen starch degradability of small and large particles of corn or barley meals

(2016) A. Gallo et al.   JOURNAL OF DAIRY SCIENCE

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

(2016) Rainer Roehe et al.   PLoS Genetics

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

(2016) Janine Kamke et al.   Microbiome

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

(2015) Analice C. Azevedo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

(2015) Kelsea A. Jewell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The rumen microbial metagenome associated with high methane production in cattle

(2015) R. John Wallace et al.   BMC GENOMICS

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Incorporating heifer feed efficiency in the Australian selection index using genomic selection

(2014) O. Gonzalez-Recio et al.   JOURNAL OF DAIRY SCIENCE

Machine learning methods and predictive ability metrics for genome-wide prediction of complex traits

(2014) Oscar González-Recio et al.   Livestock Science

Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production

(2013) J. A. Basarab et al.   Animal

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

(2013) Zhi Li et al.   BMC MICROBIOLOGY

The effect of changing cow production and fitness traits on net income and greenhouse gas emissions from Australian dairy systems

(2013) M.J. Bell et al.   JOURNAL OF DAIRY SCIENCE

Effect of dietary forage sources on rumen microbiota, rumen fermentation and biogenic amines in dairy cows

(2013) Ruiyang Zhang et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle

(2013) Elizabeth M. Ross 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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions, as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis

(2010) M. Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Assessment of the Microbial Ecology of Ruminal Methanogens in Cattle with Different Feed Efficiencies

(2009) M. Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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