PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Coastal marine habitats harbor novel early-diverging fungal diversity

(2017) Kathryn T. Picard   Fungal Ecology

Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep

(2017) Radwa A. Hanafy et al.   MYCOLOGIA

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?

(2017) Roland Marmeisse et al.   TRENDS IN BIOTECHNOLOGY

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

(2017) Chijioke O. Elekwachi et al.   Frontiers in 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

Eukaryotic community diversity and spatial variation during drinking water production (by seawater desalination) and distribution in a full-scale network

(2017) A. Belila et al.   Environmental Science-Water Research & Technology

A parts list for fungal cellulosomes revealed by comparative genomics

(2017) Charles H. Haitjema et al.   Nature Microbiology

The legacy effect of cover crops on soil fungal populations in a cereal rotation

(2016) Andrew P. Detheridge et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau

(2016) Ya-Qin Wei et al.   ANAEROBE

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi

(2016) Kevin V. Solomon et al.   ANAEROBE

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China

(2016) Xuewei Wang et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa

(2016) Guo Jie Li et al.   FUNGAL DIVERSITY

Isolation, identification and fibrolytic characteristics of rumen fungi grown with indigenous methanogen from yaks (Bos grunniens) grazing on the Qinghai-Tibetan Plateau

(2016) Y.-Q. Wei et al.   JOURNAL OF APPLIED MICROBIOLOGY

A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates

(2016) Shelby Calkins et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Development of three specific PCR-based tools to determine quantity, cellulolytic transcriptional activity and phylogeny of anaerobic fungi

(2016) Veronika Dollhofer et al.   JOURNAL OF MICROBIOLOGICAL METHODS

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

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

(2016) Kevin V. Solomon et al.   SCIENCE

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

(2016) Fuyong Li et al.   Frontiers in Microbiology

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

(2016) Magnus Ivarsson et al.   Frontiers in Microbiology

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat

(2016) D. W. Pitta et al.   Frontiers in Microbiology

Microbial communities for bioprocessing: lessons learned from nature

(2016) Xuefeng “Nick” Peng et al.   Current Opinion in Chemical Engineering

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

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

(2016) Christian Wurzbacher et al.   MycoKeys

FinisherSC: a repeat-aware tool for upgradingde novoassembly using long reads

(2015) Ka-Kit Lam et al.   BIOINFORMATICS

Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

(2015) M. B. Couger et al.   Biotechnology for Biofuels

A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius)

(2015) Sumit S. Dagar et al.   Fungal Biology

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

(2015) Hiran A. Ariyawansa et al.   FUNGAL DIVERSITY

Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples

(2015) Peter Feist et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages

(2015) S.M. Lee et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

Role of live microbial feed supplements with reference to anaerobic fungi in ruminant productivity: A review

(2015) Anil K Puniya et al.   Journal of Integrative Agriculture

The Role of Ciliate Protozoa in the Rumen

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

Driving biomass breakdown through engineered cellulosomes

(2015) Sean P Gilmore et al.   Bioengineered

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces

(2015) Gareth Wyn Griffith et al.   MycoKeys

Finding a robust strain for biomethanation: Anaerobic fungi (Neocallimastigomycota) from the Alpine ibex (Capra ibex) and their associated methanogens

(2014) Stefanie Leis et al.   ANAEROBE

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

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

Analysis of Functional Genes in Carbohydrate Metabolic Pathway of Anaerobic Rumen Fungus Neocallimastix frontalis PMA02

(2014) Mi Kwon et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production

(2014) Charles H. Haitjema et al.   BIOTECHNOLOGY AND BIOENGINEERING

Anaerobic fungi (phylumNeocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential

(2014) Robert J. Gruninger et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2014) Christian Koetschan et al.   PLoS One

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

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows

(2013) Lingling Wang et al.   PLoS One

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

(2013) Morten Poulsen et al.   Nature Communications

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

Enhanced biogas yield from energy crops with rumen anaerobic fungi

(2012) Jindřich Procházka et al.   ENGINEERING IN LIFE SCIENCES

Quantitative methods for the analysis of zoosporic fungi

(2012) Agostina V. Marano et al.   JOURNAL OF MICROBIOLOGICAL METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Sandra Kittelmann et al.   PLoS One

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

(2012) Phillip B. Pope et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2

(2011) Mark A. Buchheim et al.   ANNALS OF BOTANY

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

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

Isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane

(2011) Wei Jin et al.   BIORESOURCE TECHNOLOGY

Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases

(2011) Pan Wang et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

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

Synchronization of cell cycle of Saccharomyces cerevisiae by using a cell chip platform

(2011) Jae Young Hur et al.   MOLECULES AND CELLS

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

(2011) Mark A. Buchheim et al.   PLoS One

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

Fermentative characteristics and fibrolytic activities of anaerobic gut fungi isolated from wild and domestic ruminants

(2010) Shyam S. Paul et al.   ARCHIVES OF ANIMAL NUTRITION

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

(2010) Alexander Keller et al.   Biology Direct

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

(2010) Khin Ohnmar Lwin et al.   CURRENT MICROBIOLOGY

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

Diversity of anaerobic fungi within cow manure determined by ITS1 analysis

(2010) K. Fliegerová et al.   FOLIA MICROBIOLOGICA

Patterns of fungal diversity and composition along a salinity gradient

(2010) Devon J Mohamed et al.   ISME Journal

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

Molecular Characterization of Coprophilous Fungal Communities Reveals Sequences Related to Root-Associated Fungal Endophytes

(2010) José Herrera et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Effect of administration of rumen fungi on production performance of lactating buffaloes

(2010) S. Saxena et al.   Beneficial Microbes

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss 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

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

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.  

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments

(2008) M. Wolf et al.   BIOINFORMATICS

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

(2008) Joan E. Edwards 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