Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle

(2017) V. Lyju Jose et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet

(2017) Sophie Comtet-Marre et al.   Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen

(2017) Henk J. van Lingen et al.   Frontiers in Microbiology

A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments

(2017) Simon Deusch et al.   Frontiers in Microbiology

Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances

(2017) Amlan Patra et al.   Journal of Animal Science and Biotechnology

The ruminal microbiome associated with methane emissions from ruminant livestock

(2017) Ilma Tapio et al.   Journal of Animal Science and Biotechnology

High environmental temperature around farrowing induced heat stress in crated sows

(2016) R. Muns et al.   JOURNAL OF ANIMAL SCIENCE

Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality

(2016) Santiago Soliveres et al.   NATURE

Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol

(2016) Evert C. Duin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

(2016) Fuyong Li et al.   Frontiers in Microbiology

Microbial ecology: Linking omics to biogeochemistry

(2016) Joshua Schimel   Nature Microbiology

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure

(2016) Felix Beulig et al.   Nature Microbiology

Ruminococcal cellulosome systems from rumen to human

(2015) Yonit Ben David et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Dietary Nitrate for Methane Mitigation Leads to Nitrous Oxide Emissions from Dairy Cows

(2015) S. O. Petersen et al.   JOURNAL OF ENVIRONMENTAL QUALITY

Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming

(2015) Alexander Tøsdal Tveit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Role of Ciliate Protozoa in the Rumen

(2015) Charles J. Newbold et al.   Frontiers in Microbiology

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

(2015) Paul J. Weimer   Frontiers in Microbiology

Lambs Fed Fresh Winter Forage Rape (Brassica napus L.) Emit Less Methane than Those Fed Perennial Ryegrass (Lolium perenne L.), and Possible Mechanisms behind the Difference

(2015) Xuezhao Sun et al.   PLoS One

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

(2014) Kristina Lang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Heatmap3: an improved heatmap package with more powerful and convenient features

(2014) Shilin Zhao et al.   BMC BIOINFORMATICS

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

(2014) Guillaume Borrel et al.   BMC GENOMICS

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

(2014) Weibing Shi et al.   GENOME RESEARCH

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

(2014) Nicole Reichardt et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep

(2014) Sandra Kittelmann et al.   PLoS One

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

New aspects and strategies for methane mitigation from ruminants

(2013) Sanjay Kumar et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SPECIAL TOPICS — Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options1

(2013) A. N. Hristov et al.   JOURNAL OF ANIMAL SCIENCE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

(2012) Kristina Paul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Technical note: Test of a low-cost and animal-friendly system for measuring methane emissions from dairy cows

(2012) A.L.F. Hellwing et al.   JOURNAL OF DAIRY SCIENCE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Enteric methane mitigation technologies for ruminant livestock: a synthesis of current research and future directions

(2011) Amlan Kumar Patra   ENVIRONMENTAL MONITORING AND ASSESSMENT

Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets

(2011) Jeyamalar Jeyanathan et al.   FEMS MICROBIOLOGY ECOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

Quantitative analysis of a deeply sequenced marine microbial metatranscriptome

(2010) Scott M Gifford et al.   ISME Journal

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea

(2008) Yuchen Liu et al.   Annals of the New York Academy of Sciences

Structure of the Archaeal Community of the Rumen

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

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA