Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Using video microscopy to improve quantitative estimates of protozoal motility and cell volume

(2018) B.A. Wenner et al.   JOURNAL OF DAIRY SCIENCE

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

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

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

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

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

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

(2017) Olov Svartström et al.   ISME Journal

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

(2017) Francesco Rubino et al.   ISME Journal

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

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

(2017) Ilma Tapio et al.   PLoS One

Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture

(2017) Samantha J. Noel et al.   PLoS One

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle

(2017) Gabriel O. Ribeiro et al.   Scientific Reports

Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen

(2016) Takumi Shinkai et al.   ANIMAL SCIENCE JOURNAL

Ruminal Methanogen Community in Dairy Cows Fed Agricultural Residues of Corn Stover, Rapeseed, and Cottonseed Meals

(2016) Pengpeng Wang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Age and feeding system (supplemental feeding versus grazing) modulates colonic bacterial succession and host mucosal immune maturation in goats1

(2016) J. Jiao et al.   JOURNAL OF ANIMAL SCIENCE

Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants

(2016) Junhua Liu et al.   JOURNAL OF DAIRY SCIENCE

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers

(2016) Phillip R. Myer et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Ruminal bacterial community changes during adaptation of goats to fresh alfalfa forage

(2016) Diego Javier Grilli et al.   Livestock Science

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

(2016) Kevin V. Solomon et al.   SCIENCE

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss 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

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

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

Exploring the Goat Rumen Microbiome from Seven Days to Two Years

(2016) Lizhi Wang et al.   PLoS One

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

(2015) Sandra Kittelmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Considerations in the use of fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy to characterize rumen methanogens and define their spatial distributions

(2015) Edith R. Valle et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture

(2014) D.W. Pitta et al.   ANAEROBE

Influence of rumen protozoa on methane emission in ruminants: a meta-analysis approach

(2014) J. Guyader et al.   Animal

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

(2014) Xin Dai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

(2014) Christian Koetschan et al.   PLoS One

Determining the culturability of the rumen bacterial microbiome

(2014) Christopher J. Creevey et al.   Microbial Biotechnology

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

(2013) Noha H. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploring the bovine rumen bacterial community from birth to adulthood

(2013) Elie Jami et al.   ISME Journal

Rumen microbial (meta)genomics and its application to ruminant production

(2012) D. P. Morgavi et al.   Animal

Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets

(2012) Asma Zened et al.   FEMS MICROBIOLOGY ECOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Shifts in the Rumen Microbiota Due to the Type of Carbohydrate and Level of Protein Ingested by Dairy Cattle Are Associated with Changes in Rumen Fermentation

(2012) Alejandro Belanche et al.   JOURNAL OF NUTRITION

Activity-Based Metagenomic Screening and Biochemical Characterization of Bovine Ruminal Protozoan Glycoside Hydrolases

(2011) Seth D. Findley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiome analysis of dairy cows fed pasture or total mixed ration diets

(2011) Alexandre B. de Menezes et al.   FEMS MICROBIOLOGY ECOLOGY

Study of the effect of presence or absence of protozoa on rumen fermentation and microbial protein contribution to the chyme1

(2011) A. Belanche et al.   JOURNAL OF ANIMAL SCIENCE

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

(2011) Meng Qi et al.   PLoS One

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages

(2010) Yunhong Kong et al.   FEMS MICROBIOLOGY ECOLOGY

Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing1

(2010) T. R. Callaway et al.   JOURNAL OF ANIMAL SCIENCE

Invited review: Ruminant ecology and evolution: Perspectives useful to ruminant livestock research and production

(2010) T.J. Hackmann et al.   JOURNAL OF DAIRY SCIENCE

Population structure of rumen Escherichia coli associated with subacute ruminal acidosis (SARA) in dairy cattle

(2010) E. Khafipour et al.   JOURNAL OF DAIRY SCIENCE

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

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

Structure of the Archaeal Community of the Rumen

(2008) P. H. Janssen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen

(2008) Joan E. Edwards et al.   FEMS MICROBIOLOGY ECOLOGY

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY