Using Structural Equation Modeling to Understand Interactions Between Bacterial and Archaeal Populations and Volatile Fatty Acid Proportions in the Rumen

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages

(2021) Lucia Bailoni et al.   Microorganisms

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks

(2019) Steven D. Mamet et al.   ISME Journal

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

(2019) Alan W. Bowsher et al.   mSystems

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Syntrophy emerges spontaneously in complex metabolic systems

(2019) Eric Libby et al.   PLoS Computational Biology

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

(2019) Fuyong Li et al.   Microbiome

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

(2019) R. John Wallace et al.   Science Advances

Methylotrophic methanogens everywhere — physiology and ecology of novel players in global methane cycling

(2019) Andrea Söllinger et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Effects of 3-nitrooxypropanol on rumen fermentation, lactational performance, and resumption of ovarian cyclicity in dairy cows

(2019) A. Melgar et al.   JOURNAL OF DAIRY SCIENCE

Redox potential: An intrinsic parameter of the rumen environment

(2018) Y. Huang et al.   JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION

Symposium review: Understanding diet–microbe interactions to enhance productivity of dairy cows

(2018) Dipti W. Pitta et al.   JOURNAL OF DAIRY SCIENCE

Archaea Are Interactive Components of Complex Microbiomes

(2018) Christine Moissl-Eichinger et al.   TRENDS IN MICROBIOLOGY

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

(2018) Andrea Söllinger et al.   mSystems

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period

(2017) Zhigang Zhu et al.   PLoS One

The ruminal microbiome associated with methane emissions from ruminant livestock

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

Happy together: microbial communities that hook up to swap electrons

(2016) Derek R Lovley   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

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

(2016) Fuyong Li et al.   Frontiers in Microbiology

Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

(2016) Henry A. Paz et al.   Frontiers in Microbiology

Changes in glucose fermentation pathways by an enriched bacterial culture in response to regulated dissolved H2concentrations

(2015) Hang Zheng et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome

(2015) Marta Pozuelo et al.   Scientific Reports

Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation

(2015) Emilio M. Ungerfeld   Frontiers in Microbiology

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

(2014) Weibing Shi et al.   GENOME RESEARCH

Temporal dynamics in the ruminal microbiome of dairy cows during the transition period

(2014) D. W. Pitta et al.   JOURNAL OF ANIMAL SCIENCE

The Challenges of Studying the Anaerobic Microbial World

(2014) Koji Mori et al.   MICROBES AND ENVIRONMENTS

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Exploring the bovine rumen bacterial community from birth to adulthood

(2013) Elie Jami et al.   ISME Journal

Identification of metabolically active proteobacterial and archaeal communities in the rumen by DNA- and RNA-derived 16S rRNA gene

(2013) S.H. Kang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Diet-Induced Alterations in Total and Metabolically Active Microbes within the Rumen of Dairy Cows

(2013) Abderzak Lettat et al.   PLoS One

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

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

(2011) Daniel McDonald et al.   ISME Journal

Influence of hydrogen on rumen methane formation and fermentation balances through microbial growth kinetics and fermentation thermodynamics

(2010) Peter H. Janssen   ANIMAL FEED SCIENCE AND TECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Effects of lauric and myristic acids on ruminal fermentation, production, and milk fatty acid composition in lactating dairy cows

(2010) A.N. Hristov et al.   JOURNAL OF DAIRY SCIENCE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

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

Methanogenic archaea: ecologically relevant differences in energy conservation

(2008) Rudolf K. Thauer et al.   NATURE REVIEWS MICROBIOLOGY