Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH

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

Impact of Saccharomyces cerevisiae fermentation product and subacute ruminal acidosis on production, inflammation, and fermentation in the rumen and hindgut of dairy cows

(2016) S. Li et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community

(2016) J.X. Xiao et al.   JOURNAL OF DAIRY SCIENCE

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

(2015) Christine G. Elsik et al.   NUCLEIC ACIDS RESEARCH

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

(2015) Gemma Henderson et al.   Scientific Reports

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

(2015) Paul J. Weimer   Frontiers in Microbiology

Vitamin B 12 as a Modulator of Gut Microbial Ecology

(2014) Patrick H. Degnan et al.   Cell Metabolism

Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge

(2014) Renee M. Petri et al.   PLoS One

Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome

(2014) Abdessamad El Kaoutari et al.   PLoS One

Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing

(2013) S.Y. Mao et al.   ANAEROBE

Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product

(2013) C.R. Mullins et al.   JOURNAL OF DAIRY SCIENCE

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

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

Subacute ruminal acidosis (SARA), endotoxins and health consequences

(2012) J.C. Plaizier et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing

(2012) Hein Min Tun et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Role of vitamin B12 on methylmalonyl-CoA mutase activity

(2012) Tóshiko Takahashi-Iñiguez et al.   Journal of Zhejiang University-SCIENCE B

High throughput sequencing methods for microbiome profiling: application to food animal systems

(2012) Sarah K. Highlander   ANIMAL HEALTH RESEARCH REVIEWS

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows

(2011) Sarah E. Hook et al.   FEMS MICROBIOLOGY ECOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet

(2010) S. C. Fernando et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Rumen Microbiome Composition Determined Using Two Nutritional Models of Subacute Ruminal Acidosis

(2009) E. Khafipour et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Subacute ruminal acidosis in dairy cows: The physiological causes, incidence and consequences

(2008) J.C. Plaizier et al.   VETERINARY JOURNAL