Persistence of Cellulolytic Bacteria Fibrobacter and Treponema After Short-Term Corn Stover-Based Dietary Intervention Reveals the Potential to Improve Rumen Fibrolytic Function

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

(2017) Francesco Rubino et al.   ISME Journal

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

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

Persistent microbiome alterations modulate the rate of post-dieting weight regain

(2016) Christoph A. Thaiss et al.   NATURE

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

(2016) Gemma Henderson et al.   Scientific Reports

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

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

(2015) Paul J. Weimer   Frontiers in Microbiology

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Pectin Induces an In Vitro Rumen Microbial Population Shift Attributed to the Pectinolytic Treponema Group

(2014) Jing Liu et al.   CURRENT MICROBIOLOGY

Improved culturability of cellulolytic rumen bacteria and phylogenetic diversity of culturable cellulolytic and xylanolytic bacteria newly isolated from the bovine rumen

(2014) Thet Nyonyo et al.   FEMS MICROBIOLOGY ECOLOGY

Exploring the bovine rumen bacterial community from birth to adulthood

(2013) Elie Jami et al.   ISME Journal

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

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

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

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

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

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Isolation of Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans from rumen of Creole goats fed native forage diet

(2012) D. J. Grilli et al.   FOLIA MICROBIOLOGICA

The Fibrobacteres: an Important Phylum of Cellulose-Degrading Bacteria

(2012) Emma Ransom-Jones et al.   MICROBIAL ECOLOGY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

(2012) Xin Dai et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Detection and identification of rumen bacteria constituting a fibrolytic consortium dominated byFibrobacter succinogenes

(2010) Takumi SHINKAI et al.   ANIMAL SCIENCE JOURNAL

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis

(2010) Aschalew Z. Bekele et al.   FEMS MICROBIOLOGY LETTERS

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Development of a RT-qPCR method for the quantification of Fibrobacter succinogenes S85 glycoside hydrolase transcripts in the rumen content of gnotobiotic and conventional sheep

(2009) Christel Béra-Maillet et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One