Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

(2012) Benoit St-Pierre et al.   BMC MICROBIOLOGY

The Fibrobacteres: an Important Phylum of Cellulose-Degrading Bacteria

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

Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

(2012) Elie Jami et al.   PLoS One

Perturbation Dynamics of the Rumen Microbiota in Response to Exogenous Butyrate

(2012) Robert W. Li et al.   PLoS One

A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

(2012) Sandra Kittelmann et al.   PLoS One

Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil

(2011) Isabel S. Cunha et al.   ANAEROBE

Molecular identification of rumen methanogens: Technologies, advances and prospects

(2011) M. Zhou et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Does the complexity of the rumen microbial ecology preclude methane mitigation?

(2011) André-Denis G. Wright et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Analysis of methanogenic archaeal communities of rumen fluid and rumen particles from Korean black goats

(2011) Min-Jung GU et al.   ANIMAL SCIENCE JOURNAL

Quantification of Propionibacterium acidipropionici P169 Bacteria in Environmental Samples by Use of Strain-Specific Primers Derived by Suppressive Subtractive Hybridization

(2011) Min Peng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Differences in the Rumen Methanogen Populations of Lactating Jersey and Holstein Dairy Cows under the Same Diet Regimen

(2011) Erin E. King et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.

(2011) Sumit S. Dagar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and abundance of the rumen and fecal methanogens in Altay sheep native to Xinjiang and the influence of diversity on methane emissions

(2011) C. Liu et al.   ARCHIVES OF MICROBIOLOGY

Dasytricha Dominance in Surti Buffalo Rumen Revealed by 18S rRNA Sequences and Real-Time PCR Assay

(2011) K. M. Singh et al.   CURRENT MICROBIOLOGY

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius)

(2011) Anjas A. Samsudin et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Jeyamalar Jeyanathan et al.   FEMS MICROBIOLOGY ECOLOGY

Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis

(2011) Prem Prashant Chaudhary et al.   GENE

A ‘universal’ type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

(2011) Bonnie Chaban et al.   ISME Journal

Novel application of the MSSCP method in biodiversity studies

(2011) Karolina Tomczyk-Żak et al.   JOURNAL OF BASIC MICROBIOLOGY

Rethinking microbial diversity analysis in the high throughput sequencing era

(2011) Leandro N. Lemos et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The use of nucleic acid based stable isotope probing to identify the microorganisms responsible for anaerobic benzene and toluene biodegradation

(2011) Alison M. Cupples   JOURNAL OF MICROBIOLOGICAL METHODS

Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods

(2011) Lisa Tymensen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Methyl coenzyme M reductase (mcrA) gene based phylogenetic analysis of methanogens population in Murrah buffaloes (Bubalus bubalis)

(2011) Prem Prashant Chaudhary et al.   JOURNAL OF MICROBIOLOGY

Diversity of anaerobic fungi and rumen fermentation characteristic in swamp buffalo and beef cattle fed on different diets

(2011) P. Khejornsart et al.   Livestock Science

Ovine Ruminal Microbes Are Capable of Biotransforming Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX)

(2011) H. L. Eaton et al.   MICROBIAL ECOLOGY

Impact of High-Concentrate Feeding and Low Ruminal pH on Methanogens and Protozoa in the Rumen of Dairy Cows

(2011) Sarah E. Hook et al.   MICROBIAL ECOLOGY

Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study

(2011) Krishna M. Singh et al.   MOLECULAR BIOLOGY REPORTS

Molecular diversity of bacteria in Yunnan yellow cattle (Bos taurs) from Nujiang region, China

(2011) J. Leng et al.   MOLECULAR BIOLOGY REPORTS

Enumeration of methanogens with a focus on fluorescence in situ hybridization

(2011) Sanjay Kumar et al.   NATURWISSENSCHAFTEN

Confirmation of the paraphyletic relationship between families Opisthorchiidae and Heterophyidae using small and large subunit ribosomal DNA sequences

(2011) Urusa Thaenkham et al.   PARASITOLOGY INTERNATIONAL

Cellulosomics, a Gene-Centric Approach to Investigating the Intraspecific Diversity and Adaptation of Ruminococcus flavefaciens within the Rumen

(2011) Jennifer M. Brulc et al.   PLoS One

Anaerobic fungi: Neocallimastigomycota

(2011) Gareth W Griffith et al.   IMA Fungus

Bacterial and Protozoal Communities and Fatty Acid Profile in the Rumen of Sheep Fed a Diet Containing Added Tannins

(2010) V. Vasta et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cellulosilyticum ruminicola, a Newly Described Rumen Bacterium That Possesses Redundant Fibrolytic-Protein-Encoding Genes and Degrades Lignocellulose with Multiple Carbohydrate- Borne Fibrolytic Enzymes

(2010) S. Cai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative Fluorescence In Situ Hybridization of Microbial Communities in the Rumens of Cattle Fed Different Diets

(2010) Y. Kong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions, as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis

(2010) M. Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Real-Time PCR Assays for Monitoring Anaerobic Fungal Biomass and Population Size in the Rumen

(2010) Khin Ohnmar Lwin et al.   CURRENT MICROBIOLOGY

The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs

(2010) David R. Yáñez-Ruiz et al.   FEMS MICROBIOLOGY ECOLOGY

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

Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries

(2010) Sandra Kittelmann et al.   FEMS MICROBIOLOGY ECOLOGY

Diversity of anaerobic fungi within cow manure determined by ITS1 analysis

(2010) K. Fliegerová et al.   FOLIA MICROBIOLOGICA

Rumen methanogens: a review

(2010) S. K. Sirohi et al.   INDIAN JOURNAL OF MICROBIOLOGY

Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores

(2010) Audra S Liggenstoffer et al.   ISME Journal

Diversity of Rumen Anaerobic Fungi and Methanogenic Archaea in Swamp Buffalo Influenced by Various Diets

(2010) Pichad Khejornsar et al.   Journal of Animal and Veterinary Advances

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

Molecular Identification of Veterinary Yeast Isolates by Use of Sequence-Based Analysis of the D1/D2 Region of the Large Ribosomal Subunit

(2010) C. D. Garner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

pH dynamics and bacterial community composition in the rumen of lactating dairy cows

(2010) A. Palmonari et al.   JOURNAL OF DAIRY SCIENCE

Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond

(2010) J. Rajendhran et al.   MICROBIOLOGICAL RESEARCH

Assessment of protozoa in Yunnan Yellow Cattle rumen based on the 18S rRNA sequences

(2010) J. Leng et al.   MOLECULAR BIOLOGY REPORTS

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

(2010) Sinead C. Leahy et al.   PLoS One

When metagenomics meets stable-isotope probing: progress and perspectives

(2010) Yin Chen et al.   TRENDS IN MICROBIOLOGY

Methanogens: Methane Producers of the Rumen and Mitigation Strategies

(2010) Sarah E. Hook et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores

(2009) Matthew J. Nicholson et al.   ANAEROBE

ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle

(2009) David G. Welkie et al.   ANAEROBE

mcrA-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities

(2009) L. M. Steinberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community Composition and Density of Methanogens in the Foregut of the Tammar Wallaby (Macropus eugenii)

(2009) P. N. Evans et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture

(2009) Yan Fen Cheng et al.   BIORESOURCE TECHNOLOGY

Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources

(2009) G.W. Griffith et al.   Fungal Ecology

Molecular diversity analysis of rumen methanogenicArchaeafrom goat in eastern China by DGGE methods using different primer pairs

(2009) Y.F. Cheng et al.   LETTERS IN APPLIED MICROBIOLOGY

Dominance ofMethanomicrobiumphylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis)

(2009) P.P. Chaudhary et al.   LETTERS IN APPLIED MICROBIOLOGY

Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks (Bos grunniens)

(2009) L. Y. Yang et al.   MOLECULAR BIOLOGY REPORTS

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Factors affecting rumen methanogens and methane mitigation strategies

(2009) Sanjay Kumar et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems

(2009) Mohammad H. Sekhavati et al.  

The Cellulase/Hemicellulase System of the Anaerobic FungusOrpinomycesPC-2 and Aspects of Its Applied Use

(2008) Lars G. Ljungdahl   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

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

(2008) Ursel M. E. Schütte et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Methanogen genomics to discover targets for methane mitigation technologies and options for alternative H2utilisation in the rumen

(2008) Graeme Attwood et al.   Australian journal of experimental agriculture

Use of Real-Time PCR Technique in Studying Rumen Cellulolytic Bacteria Population as Affected by Level of Roughage in Swamp Buffalo

(2008) Metha Wanapat et al.   CURRENT MICROBIOLOGY

Rumen protozoal diversity in the Spanish ibex (Capra pyrenaica hispanica) as compared with domestic goats (Capra hircus)

(2008) Gabriel de la Fuente et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

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

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

Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen

(2008) James B. Russell et al.   FEMS MICROBIOLOGY ECOLOGY

Detection and monitoring of anaerobic rumen fungi using an ARISA method

(2008) S.E. Denman et al.   LETTERS IN APPLIED MICROBIOLOGY

Molecular Diversity of the Rumen Microbiome of Norwegian Reindeer on Natural Summer Pasture

(2008) Monica A. Sundset et al.   MICROBIAL ECOLOGY

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY

A serpin in the cellulosome of the anaerobic fungus Piromyces sp. strain E2

(2008) Peter J.M. Steenbakkers et al.