Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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

Abstract

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond themore » broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Finally, once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.« less

Authors:
 [1];  [2];  [3];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [10];  [10];  [11];  [1]
+ Show Author Affiliations
  1. Wageningen Univ. & Research, Wageningen (Netherlands). Lab. of Microbiology
  2. Agriculture and Agri-Food Canada, Lethbridge, AB (Canada). Lethbridge Research and Development Centre
  3. Bavarian State Research Center for Agriculture, Freising (Germany). Dept. for Quality Assurance and Analytics
  4. Agharkar Research Inst., Pune (India). Bioenergy Group
  5. Nanjing Agricultural Univ., Nanjing (China). Lab. of Gastrointestinal Microbiology
  6. Korea National Open Univ., Seoul (South Korea). Dept. of Agricultural Science
  7. AgResearch Ltd., Palmerston North (New Zealand). Grasslands Research Centre
  8. Czech Academy of Sciences, Prague (Czechia). Inst. of Animal Physiology and Genetics
  9. Guru Angad Dev Veterinary and Animal Sciences Univ., Ludhiana (India). College of Dairy Science and Technology; CAR-National Dairy Research Inst., Karnal (India). Dairy Microbiology Division
  10. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering
  11. Aberystwyth Univ., Aberystwyth (United Kingdom). Inst. of Biological Environmental and Rural Sciences
Publication Date:
Research Org.:
Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); European Union (EU); National Science Foundation (NSF)
OSTI Identifier:
1424614
Grant/Contract Number:  
SC0010352; AC02-05CH11231; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anerobic fungi; Neocallimastigomycota; rumen; phylogeny; genomics; (meta) transcriptomics; proteomics; metabolomics

Citation Formats

Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., and Smidt, Hauke. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.01657.
Copy to clipboard
Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., & Smidt, Hauke. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. United States. https://doi.org/10.3389/fmicb.2017.01657
Copy to clipboard
Edwards, Joan E., Forster, Robert J., Callaghan, Tony M., Dollhofer, Veronika, Dagar, Sumit S., Cheng, Yanfen, Chang, Jongsoo, Kittelmann, Sandra, Fliegerova, Katerina, Puniya, Anil K., Henske, John K., Gilmore, Sean P., O'Malley, Michelle A., Griffith, Gareth W., and Smidt, Hauke. Mon . "PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities". United States. https://doi.org/10.3389/fmicb.2017.01657. https://www.osti.gov/servlets/purl/1424614.
Copy to clipboard
@article{osti_1424614,
title = {PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities},
author = {Edwards, Joan E. and Forster, Robert J. and Callaghan, Tony M. and Dollhofer, Veronika and Dagar, Sumit S. and Cheng, Yanfen and Chang, Jongsoo and Kittelmann, Sandra and Fliegerova, Katerina and Puniya, Anil K. and Henske, John K. and Gilmore, Sean P. and O'Malley, Michelle A. and Griffith, Gareth W. and Smidt, Hauke},
abstractNote = {Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Finally, once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.},
doi = {10.3389/fmicb.2017.01657},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {9}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fmicb.2017.01657
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 68 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Analysis of restriction fragment length polymorphisms in the ribosomal DNA of a selection of anaerobic chytrids
journal, July 2000

  • Hausner, G.; Inglis, G. D.; Yanke, L. J.
  • Canadian Journal of Botany, Vol. 78, Issue 7
  • DOI: 10.1139/b00-067

Metabolomics applied in bioenergy
journal, October 2014

  • Abdelnur, Patricia V.; Caldana, Camila; Martins, Marina C. M.
  • Chemical and Biological Technologies in Agriculture, Vol. 1, Issue 1
  • DOI: 10.1186/s40538-014-0022-0

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
journal, January 2010

  • Keller, Alexander; Förster, Frank; Müller, Tobias
  • Biology Direct, Vol. 5, Issue 1
  • DOI: 10.1186/1745-6150-5-4

Quantitative methods for the analysis of zoosporic fungi
journal, April 2012

  • Marano, Agostina V.; Gleason, Frank H.; Bärlocher, Felix
  • Journal of Microbiological Methods, Vol. 89, Issue 1
  • DOI: 10.1016/j.mimet.2012.02.003

Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen: Initial colonization of forage by ruminal anaerobic fungi
journal, December 2008

Growth of Anaerobic Rumen Fungi on Defined and Semi-defined Media Lacking Rumen Fluid
journal, September 1985

A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius)
journal, August 2015

Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose.
journal, October 1987

  • Aebersold, R. H.; Leavitt, J.; Saavedra, R. A.
  • Proceedings of the National Academy of Sciences, Vol. 84, Issue 20
  • DOI: 10.1073/pnas.84.20.6970

Anaerobic fungi (phylum Neocallimastigomycota ): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential
journal, August 2014

  • Gruninger, Robert J.; Puniya, Anil K.; Callaghan, Tony M.
  • FEMS Microbiology Ecology, Vol. 90, Issue 1
  • DOI: 10.1111/1574-6941.12383

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces
journal, March 2015

Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa
journal, May 2016

Molecular Biological Detection of Anaerobic Gut Fungi (Neocallimastigales) from Landfill Sites
journal, August 2006

  • Lockhart, R. J.; Van Dyke, M. I.; Beadle, I. R.
  • Applied and Environmental Microbiology, Vol. 72, Issue 8
  • DOI: 10.1128/AEM.01057-06

Synchronization of cell cycle of Saccharomyces cerevisiae by using a cell chip platform
journal, November 2011

Patterns of fungal diversity and composition along a salinity gradient
journal, September 2010

Penetrating Structures of Anaerobic Rumen Fungi in Cattle and Swamp Buffalo
journal, January 1988

Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores
journal, April 2010

  • Liggenstoffer, Audra S.; Youssef, Noha H.; Couger, M. B.
  • The ISME Journal, Vol. 4, Issue 10
  • DOI: 10.1038/ismej.2010.49

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems
journal, October 2009

  • Sekhavati, Mohammad H.; Mesgaran, Mohsen Danesh; Nassiri, Mohammad R.
  • Mycological Research, Vol. 113, Issue 10
  • DOI: 10.1016/j.mycres.2009.07.017

Presence in rumen bacterial and protozoal populations of enzymes capable of degrading fungal cell walls
journal, March 1994

Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora: Enzymatic diversity from bovine rumen metagenome
journal, September 2005

Cloning and expression of multiple cellulase cDNAs from the anaerobic rumen fungus Neocallimastix patriciarum in Escherichia coli
journal, July 1992

Description of two anaerobic fungal strains from the bovine rumen and influence of diet on the fungal population in vivo
journal, July 1991

  • Kostyukovsky, V. A.; Okunev, O. N.; Tarakanov, B. V.
  • Journal of General Microbiology, Vol. 137, Issue 7
  • DOI: 10.1099/00221287-137-7-1759

Phylogeny of anaerobic rumen Chytridiomycetes inferred from small subunit ribosomal RNA sequence comparisons
journal, September 1991

  • Dore, J.; Stahl, D. A.
  • Canadian Journal of Botany, Vol. 69, Issue 9
  • DOI: 10.1139/b91-246

Degradation and fermentation of cellulose by the rumen anaerobic fungi in axenic cultures or in association with cellulolytic bacteria
journal, September 1992

  • Bernalier, Annick; Fonty, Gérard; Bonnemoy, Frédérique
  • Current Microbiology, Vol. 25, Issue 3
  • DOI: 10.1007/BF01571022

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat
journal, May 2016

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China
journal, October 2016

  • Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z.
  • Antonie van Leeuwenhoek, Vol. 110, Issue 1
  • DOI: 10.1007/s10482-016-0779-1

Eukaryotic community diversity and spatial variation during drinking water production (by seawater desalination) and distribution in a full-scale network
journal, January 2017

  • Belila, A.; El-Chakhtoura, J.; Saikaly, P. E.
  • Environmental Science: Water Research & Technology, Vol. 3, Issue 1
  • DOI: 10.1039/C6EW00265J

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases
journal, January 2009

  • Brulc, Jennifer M.; Antonopoulos, Dionysios A.; Berg Miller, Margret E.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
  • DOI: 10.1073/pnas.0806191105

Cellulose degradation by two rumen anaerobic fungi in monoculture or in coculture with rumen bacteria
journal, January 1991

Influence of an anaerobic fungal culture administration on in vivo ruminal fermentation and nutrient digestion
journal, December 2000

Fungal secondary metabolism — from biochemistry to genomics
journal, December 2005

  • Keller, Nancy P.; Turner, Geoffrey; Bennett, Joan W.
  • Nature Reviews Microbiology, Vol. 3, Issue 12, p. 937-947
  • DOI: 10.1038/nrmicro1286

Diversity of Rumen Anaerobic Fungi and Methanogenic Archaea in Swamp Buffalo Influenced by Various Diets
journal, December 2010

Mass spectrometry in metabolome analysis
journal, January 2005

  • Villas-Bôas, Silas G.; Mas, Sandrine; Åkesson, Mats
  • Mass Spectrometry Reviews, Vol. 24, Issue 5
  • DOI: 10.1002/mas.20032

Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle
journal, June 2001

  • Ozkose, Emin; Thomas, Barry J.; Davies, David R.
  • Canadian Journal of Botany, Vol. 79, Issue 6
  • DOI: 10.1139/b01-047

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)
journal, October 2016

The Role of Ciliate Protozoa in the Rumen
journal, November 2015

  • Newbold, Charles J.; de la Fuente, Gabriel; Belanche, Alejandro
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.01313

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes
journal, February 2016

  • Solomon, Kevin V.; Haitjema, Charles H.; Henske, John K.
  • Science, Vol. 351, Issue 6278
  • DOI: 10.1126/science.aad1431

Microbial proteomics: a mass spectrometry primer for biologists
journal, January 2007

  • Graham, Robert LJ; Graham, Ciaren; McMullan, Geoff
  • Microbial Cell Factories, Vol. 6, Issue 1
  • DOI: 10.1186/1475-2859-6-26

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi
journal, April 2016

The legacy effect of cover crops on soil fungal populations in a cereal rotation
journal, July 2016

  • Detheridge, Andrew P.; Brand, Graham; Fychan, Rhun
  • Agriculture, Ecosystems & Environment, Vol. 228
  • DOI: 10.1016/j.agee.2016.04.022

Xylanolysis by cocultures of the rumen fungus Neocallimastix frontalis and ruminal bacteria
journal, June 1991

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009

  • Schloss, P. D.; Westcott, S. L.; Ryabin, T.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
  • DOI: 10.1128/AEM.01541-09

Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production: Anaerobic Gut Fungi
journal, May 2014

  • Haitjema, Charles H.; Solomon, Kevin V.; Henske, John K.
  • Biotechnology and Bioengineering, Vol. 111, Issue 8
  • DOI: 10.1002/bit.25264

Current two-dimensional electrophoresis technology for proteomics
journal, November 2004

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
journal, January 2008

  • Seibel, Philipp N.; Müller, Tobias; Dandekar, Thomas
  • BMC Research Notes, Vol. 1, Issue 1
  • DOI: 10.1186/1756-0500-1-91

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Anaerobic fungi in the digestive tract of mammalian herbivores and their potential for exploitation
journal, November 1996

  • Theodorou, Michael K.; Mennim, Georgina; Davies, David R.
  • Proceedings of the Nutrition Society, Vol. 55, Issue 3
  • DOI: 10.1079/PNS19960088

Effect of Eubacterium limosum, a ruminal hydrogenotrophic bacterium, on the degradation and fermentation of cellulose by 3 species of rumen anaerobic fungi
journal, January 1993

  • Bernalier, A.; Fonty, G.; Bonnemoy, F.
  • Reproduction Nutrition Development, Vol. 33, Issue 6
  • DOI: 10.1051/rnd:19930609

Fermentation activities of some new species of anaerobic rumen fungi from Malaysia.
journal, January 1996

  • Ho, Yin-Wan; Wong, Michael V. -L.; Abdullan, Norhani
  • The Journal of General and Applied Microbiology, Vol. 42, Issue 1
  • DOI: 10.2323/jgam.42.51

Effect of heterotrophic ruminal bacteria on xylan metabolism by the anaerobic fungus Piromyces communis
journal, August 1994

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader
journal, May 2013

  • Youssef, Noha H.; Couger, M. B.; Struchtemeyer, Christopher G.
  • Applied and Environmental Microbiology, Vol. 79, Issue 15
  • DOI: 10.1128/AEM.00821-13

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
journal, March 2012

  • Schoch, C. L.; Seifert, K. A.; Huhndorf, S.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
  • DOI: 10.1073/pnas.1117018109

Diversity of anaerobic fungi within cow manure determined by ITS1 analysis
journal, July 2010

Distribution of anaerobic fungi in the digestive tract of cattle and their survival in faeces
journal, June 1993

  • Davies, D. R.; Theodorou, M. K.; Lawrence, M. I. G.
  • Journal of General Microbiology, Vol. 139, Issue 6
  • DOI: 10.1099/00221287-139-6-1395

Diversity of anaerobic fungi and rumen fermentation characteristic in swamp buffalo and beef cattle fed on different diets
journal, August 2011

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities
journal, September 2013

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches
journal, June 2016

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
journal, February 2013

  • Poulsen, Morten; Schwab, Clarissa; Borg Jensen, Bent
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2432

A parts list for fungal cellulosomes revealed by comparative genomics
journal, May 2017

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
journal, October 2015

  • Henderson, Gemma; Cox, Faith; Ganesh, Siva
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14567

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi: Methods
journal, March 2005

MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
journal, March 2016

  • Schurch, Nicholas J.; Schofield, Pietá; Gierliński, Marek
  • RNA, Vol. 22, Issue 6
  • DOI: 10.1261/rna.053959.115

Influence of an Anaerobic Fungal Culture (Orpinomyces sp.) Administration on Growth Rate, Ruminal Fermentation and Nutrient Digestion in Calves
journal, January 2004

  • Dey, Avijit; Sehgal, Jatinder Paul; Puniya, Anil Kumar
  • Asian-Australasian Journal of Animal Sciences, Vol. 17, Issue 6
  • DOI: 10.5713/ajas.2004.820

The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages
journal, January 2015

  • Lee, S. M.; Guan, L. L.; Eun, J. -S.
  • Journal of Applied Microbiology, Vol. 118, Issue 3
  • DOI: 10.1111/jam.12724

Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?
journal, September 2017

Driving biomass breakdown through engineered cellulosomes
journal, February 2015

The survival of anaerobic fungi in cattle faeces
journal, July 1999

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
journal, February 2011

Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together on lignocellulose in consecutive batch culture
journal, October 2009

Primary sequence and enzymic properties of two modular endoglucanases, Cel5A and Cel45A, from the anaerobic fungus Piromyces equi
journal, August 2000

Production of Citrate by Anaerobic Fungi in the Presence of Co-culture Methanogens as Revealed by 1H NMR Spectrometry
journal, January 1970

  • Cheng, Yan Fen; Jin, Wei; Mao, Sheng Yong
  • Asian-Australasian Journal of Animal Sciences, Vol. 26, Issue 10
  • DOI: 10.5713/ajas.2013.13134

Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin
journal, August 1992

Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources
journal, May 2009

Studies on the Rumen Flagellate Neocallimastix frontalis
journal, December 1975

Effect of administration of anaerobic fungi isolated from cattle and wild blue bull ( Boselaphus tragocamelus ) on growth rate and fibre utilization in buffalo calves
journal, August 2007

  • Tripathi, Vimal K.; Sehgal, Jatinder P.; Puniya, Anil K.
  • Archives of Animal Nutrition, Vol. 61, Issue 5
  • DOI: 10.1080/17450390701556759

Differential expression in RNA-seq: A matter of depth
journal, September 2011

  • Tarazona, S.; Garcia-Alcalde, F.; Dopazo, J.
  • Genome Research, Vol. 21, Issue 12
  • DOI: 10.1101/gr.124321.111

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows
journal, November 2013

Molecular Characterization of Coprophilous Fungal Communities Reveals Sequences Related to Root-Associated Fungal Endophytes
journal, September 2010

Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases
journal, July 2011

  • Wang, Pan; Qi,   Meng; Barboza,   Perry
  • Canadian Journal of Microbiology, Vol. 57, Issue 7
  • DOI: 10.1139/w11-048

Microbial metabolomics: past, present and future methodologies
journal, November 2006

GenBank
journal, November 2012

  • Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1195

Reference databases for taxonomic assignment in metagenomics
journal, July 2012

  • Santamaria, M.; Fosso, B.; Consiglio, A.
  • Briefings in Bioinformatics, Vol. 13, Issue 6
  • DOI: 10.1093/bib/bbs036

Reconstructing the early evolution of Fungi using a six-gene phylogeny
journal, October 2006

  • James, Timothy Y.; Kauff, Frank; Schoch, Conrad L.
  • Nature, Vol. 443, Issue 7113
  • DOI: 10.1038/nature05110

The Rumen Ecosystem : As a Fountain Sources of Nobel Enzymes - Review -
journal, June 1999

  • Lee, S. S.; Shin, K. J.; Kim, W. Y.
  • Asian-Australasian Journal of Animal Sciences, Vol. 12, Issue 6
  • DOI: 10.5713/ajas.1999.988

Role of live microbial feed supplements with reference to anaerobic fungi in ruminant productivity: A review
journal, March 2015

  • Puniya, Anil K.; Salem, Abdelfattah Z. M.; Kumar, Sanjay
  • Journal of Integrative Agriculture, Vol. 14, Issue 3
  • DOI: 10.1016/S2095-3119(14)60837-6

Anaerobic fungi in herbivorous animals
journal, February 1994

Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis
journal, May 2000

  • Fell, J. W.; Boekhout, T.; Fonseca, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 3
  • DOI: 10.1099/00207713-50-3-1351

Fermentative characteristics and fibrolytic activities of anaerobic gut fungi isolated from wild and domestic ruminants
journal, August 2010

  • Paul, Shyam S.; Kamra, Devki N.; Sastry, Vadali R. B.
  • Archives of Animal Nutrition, Vol. 64, Issue 4
  • DOI: 10.1080/17450391003625037

Characterizing and measuring bias in sequence data
journal, January 2013

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome
journal, January 2005

Neocallimastix patriciarum sp.nov., a new member of the Neocallimasticaceae inhabiting the rumen of sheep
journal, January 1986

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
journal, January 2017

  • Comtet-Marre, Sophie; Parisot, Nicolas; Lepercq, Pascale
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.00067

Detection and monitoring of anaerobic rumen fungi using an ARISA method
journal, December 2008

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
journal, November 2015

  • Ariyawansa, Hiran A.; Hyde, Kevin D.; Jayasiri, Subashini C.
  • Fungal Diversity, Vol. 75, Issue 1
  • DOI: 10.1007/s13225-015-0346-5

Pecoramyces ruminantium , gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep
journal, March 2017

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
journal, June 2012

The UNITE database for molecular identification of fungi - recent updates and future perspectives: Letters
journal, March 2010

Effect of administration of rumen fungi on production performance of lactating buffaloes
journal, June 2010

  • Saxena, S.; Sehgal, J.; Puniya, A.
  • Beneficial Microbes, Vol. 1, Issue 2
  • DOI: 10.3920/BM2009.0018

Development of three specific PCR-based tools to determine quantity, cellulolytic transcriptional activity and phylogeny of anaerobic fungi
journal, August 2016

  • Dollhofer, Veronika; Callaghan, Tony Martin; Dorn-In, Samart
  • Journal of Microbiological Methods, Vol. 127
  • DOI: 10.1016/j.mimet.2016.05.017

A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates
journal, August 2016

Large-scale protein identification using mass spectrometry
journal, March 2003

  • Lin, Dayin; Tabb, David L.; Yates, John R.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1646, Issue 1-2
  • DOI: 10.1016/S1570-9639(02)00546-0

Real-Time PCR Assays for Monitoring Anaerobic Fungal Biomass and Population Size in the Rumen
journal, December 2010

  • Lwin, Khin Ohnmar; Hayakawa, Mika; Ban-Tokuda, Tomomi
  • Current Microbiology, Vol. 62, Issue 4
  • DOI: 10.1007/s00284-010-9843-7

A cyclophilin from the polycentric anaerobic rumen fungus Orpinomyces sp. strain PC-2 is highly homologous to vertebrate cyclophilin B.
journal, March 1995

  • Chen, H.; Li, X. L.; Ljungdahl, L. G.
  • Proceedings of the National Academy of Sciences, Vol. 92, Issue 7
  • DOI: 10.1073/pnas.92.7.2587

Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores
journal, April 2010

Efficient production of cellulolytic and xylanolytic enzymes by the rumen anaerobic fungus, Neocallimastix frontalis, in a repeated batch culture
journal, January 2001

  • Srinivasan, Karthikeyan; Murakami, Makoto; Nakashimada, Yutaka
  • Journal of Bioscience and Bioengineering, Vol. 91, Issue 2
  • DOI: 10.1016/S1389-1723(01)80058-X

Biochemical and Microbiological Evidence for Fermentative Digestion in Free‐Living Land Iguanas ( Conolophus pallidus ) and Marine Iguanas ( Amblyrhynchus cristatus ) on the Galápagos Archipelago
journal, January 2004

  • Mackie, Roderick I.; Rycyk, Mathew; Ruemmler, Rebecca L.
  • Physiological and Biochemical Zoology, Vol. 77, Issue 1
  • DOI: 10.1086/383498

Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2
journal, October 2011

  • Buchheim, Mark A.; Sutherland, Danica M.; Schleicher, Tina
  • Annals of Botany, Vol. 109, Issue 1
  • DOI: 10.1093/aob/mcr275

Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants
journal, July 2017

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust
journal, May 2016

Coastal marine habitats harbor novel early-diverging fungal diversity
journal, February 2017

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
journal, June 2015

Sugar and polysaccharide fermentation by rumen anaerobic fungi from Australia, Britain and New Zealand
journal, January 1988

D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.
journal, July 2011

  • Dagar, Sumit S.; Kumar, Sanjay; Mudgil, Priti
  • Applied and Environmental Microbiology, Vol. 77, Issue 18
  • DOI: 10.1128/AEM.05441-11

Glucose metabolic pathways in the anaerobic rumen fungus Neocallimastix frontalis EB188
journal, March 1991

  • O'Fallon, J. V.; Wright, R. W.; Calza, R. E.
  • Biochemical Journal, Vol. 274, Issue 2
  • DOI: 10.1042/bj2740595

Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A
journal, December 2015

  • Couger, M. B.; Youssef, Noha H.; Struchtemeyer, Christopher G.
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0390-0

Metabolomics technology and bioinformatics
journal, March 2006

Special Properties of Polycentric Anaerobic Fungus Anaeromyces mucronatus
journal, January 2002

  • Fliegerová, K.; Pažoutová, S.; Mrázek, J.
  • Acta Veterinaria Brno, Vol. 71, Issue 4
  • DOI: 10.2754/avb200271040441

Enhanced biogas yield from energy crops with rumen anaerobic fungi: Increase of biogas yield by rumen fungi
journal, June 2012

  • Procházka, Jindřich; Mrázek, Jakub; Štrosová, Lenka
  • Engineering in Life Sciences, Vol. 12, Issue 3
  • DOI: 10.1002/elsc.201100076

Analysis of Functional Genes in Carbohydrate Metabolic Pathway of Anaerobic Rumen Fungus Neocallimastix frontalis PMA02
journal, October 2009

  • Kwon, Mi; Song, Jaeyong; Ha, Jong K.
  • Asian-Australasian Journal of Animal Sciences, Vol. 22, Issue 11
  • DOI: 10.5713/ajas.2009.80371

Modification of a xylanase cDNA isolated from an anaerobic fungus Neocallimastix patriciarum for high-level expression in Escherichia coli
journal, January 1995

Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples
journal, February 2015

  • Feist, Peter; Hummon, Amanda
  • International Journal of Molecular Sciences, Vol. 16, Issue 2
  • DOI: 10.3390/ijms16023537

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments
journal, August 2008

Widespread adenine N6-methylation of active genes in fungi
journal, May 2017

  • Mondo, Stephen J.; Dannebaum, Richard O.; Kuo, Rita C.
  • Nature Genetics, Vol. 49, Issue 6
  • DOI: 10.1038/ng.3859

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
journal, January 2011

Microbial communities for bioprocessing: lessons learned from nature
journal, November 2016

  • Peng, Xuefeng “Nick”; Gilmore, Sean P.; O’Malley, Michelle A.
  • Current Opinion in Chemical Engineering, Vol. 14
  • DOI: 10.1016/j.coche.2016.09.003

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach
journal, May 2011

Identification and characterization of anaerobic gut fungi using molecular methodologies based on ribosomal ITS1 and 18S rRNA
journal, February 2000

Growth and fermentation of an anaerobic rumen fungus on various carbon sources and effect of temperature on development.
journal, January 1987

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae
journal, March 2021

  • Will, Robert C.; Ramamurthy, Thandavarayan; Sharma, Naresh Chand
  • Nature Communications, Vol. 12, Issue 1
  • DOI: 10.1038/s41467-021-21870-5

Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
text, January 2021

Analysis of restriction fragment length polymorphisms in the ribosomal DNA of a selection of anaerobic chytrids
journal, January 2000

  • Hausner, G.; Inglis, G. D.; Yanke, L. J.
  • Canadian Journal of Botany, Vol. 78, Issue 7
  • DOI: 10.1139/cjb-78-7-917

Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle
journal, January 2001

  • Ozkose, Emin; Thomas, Barry J.; Davies, David R.
  • Canadian Journal of Botany, Vol. 79, Issue 6
  • DOI: 10.1139/cjb-79-6-666

Classical and molecular approaches as a powerful tool for the characterization of rumen polycentric fungi
journal, March 2004

  • Fliegerová, K.; Hodrová, B.; Voigt, K.
  • Folia Microbiologica, Vol. 49, Issue 2
  • DOI: 10.1007/bf02931392

Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP
journal, July 2006

  • Fliegerová, K.; Mrázek, J.; Voigt, K.
  • Folia Microbiologica, Vol. 51, Issue 4
  • DOI: 10.1007/bf02931811

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China
journal, October 2016

  • Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z.
  • Antonie van Leeuwenhoek, Vol. 110, Issue 1
  • DOI: 10.1007/s10482-016-0779-1

Diversity of anaerobic fungi within cow manure determined by ITS1 analysis
journal, July 2010

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
journal, November 2015

  • Ariyawansa, Hiran A.; Hyde, Kevin D.; Jayasiri, Subashini C.
  • Fungal Diversity, Vol. 75, Issue 1
  • DOI: 10.1007/s13225-015-0346-5

Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa
journal, May 2016

Sugar and polysaccharide fermentation by rumen anaerobic fungi from Australia, Britain and New Zealand
journal, January 1988

The legacy effect of cover crops on soil fungal populations in a cereal rotation
journal, July 2016

  • Detheridge, Andrew P.; Brand, Graham; Fychan, Rhun
  • Agriculture, Ecosystems & Environment, Vol. 228
  • DOI: 10.1016/j.agee.2016.04.022

Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores
journal, April 2010

Microbial communities for bioprocessing: lessons learned from nature
journal, November 2016

  • Peng, Xuefeng “Nick”; Gilmore, Sean P.; O’Malley, Michelle A.
  • Current Opinion in Chemical Engineering, Vol. 14
  • DOI: 10.1016/j.coche.2016.09.003

A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius)
journal, August 2015

Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources
journal, May 2009

Coastal marine habitats harbor novel early-diverging fungal diversity
journal, February 2017

Quantitative methods for the analysis of zoosporic fungi
journal, April 2012

  • Marano, Agostina V.; Gleason, Frank H.; Bärlocher, Felix
  • Journal of Microbiological Methods, Vol. 89, Issue 1
  • DOI: 10.1016/j.mimet.2012.02.003

A higher-level phylogenetic classification of the Fungi
journal, May 2007

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems
journal, October 2009

  • Sekhavati, Mohammad H.; Mesgaran, Mohsen Danesh; Nassiri, Mohammad R.
  • Mycological Research, Vol. 113, Issue 10
  • DOI: 10.1016/j.mycres.2009.07.017

Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?
journal, September 2017

ITS2 is a double-edged tool for eukaryote evolutionary comparisons
journal, July 2003

Distribution and estimation of anaerobic zoosporic fungi along the digestive tracts of sheep
journal, October 2004

  • Rezaeian, Mohammad; Beakes, Gordon W.; Parker, David S.
  • Mycological Research, Vol. 108, Issue 10
  • DOI: 10.1017/s0953756204000929

Patterns of fungal diversity and composition along a salinity gradient
journal, September 2010

Reconstructing the early evolution of Fungi using a six-gene phylogeny
journal, October 2006

  • James, Timothy Y.; Kauff, Frank; Schoch, Conrad L.
  • Nature, Vol. 443, Issue 7113
  • DOI: 10.1038/nature05110

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
journal, February 2013

  • Poulsen, Morten; Schwab, Clarissa; Borg Jensen, Bent
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2432

A parts list for fungal cellulosomes revealed by comparative genomics
journal, May 2017

Fungal secondary metabolism — from biochemistry to genomics
journal, December 2005

  • Keller, Nancy P.; Turner, Geoffrey; Bennett, Joan W.
  • Nature Reviews Microbiology, Vol. 3, Issue 12, p. 937-947
  • DOI: 10.1038/nrmicro1286

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
journal, October 2015

  • Henderson, Gemma; Cox, Faith; Ganesh, Siva
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14567

Effect of Eubacterium limosum, a ruminal hydrogenotrophic bacterium, on the degradation and fermentation of cellulose by 3 species of rumen anaerobic fungi
journal, January 1993

  • Bernalier, A.; Fonty, G.; Bonnemoy, F.
  • Reproduction Nutrition Development, Vol. 33, Issue 6
  • DOI: 10.1051/rnd:19930609

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases
journal, January 2009

  • Brulc, Jennifer M.; Antonopoulos, Dionysios A.; Berg Miller, Margret E.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
  • DOI: 10.1073/pnas.0806191105

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
journal, March 2012

  • Schoch, C. L.; Seifert, K. A.; Huhndorf, S.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
  • DOI: 10.1073/pnas.1117018109

The role of anaerobic gut fungi in ruminants
journal, June 1998

  • Gordon, Geoffrey L. R.; Phillips, Michael W.
  • Nutrition Research Reviews, Vol. 11, Issue 1
  • DOI: 10.1079/nrr19980009

Pecoramyces ruminantium , gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep
journal, March 2017

Effect of administration of anaerobic fungi isolated from cattle and wild blue bull ( Boselaphus tragocamelus ) on growth rate and fibre utilization in buffalo calves
journal, August 2007

  • Tripathi, Vimal K.; Sehgal, Jatinder P.; Puniya, Anil K.
  • Archives of Animal Nutrition, Vol. 61, Issue 5
  • DOI: 10.1080/17450390701556759

Fermentative characteristics and fibrolytic activities of anaerobic gut fungi isolated from wild and domestic ruminants
journal, August 2010

  • Paul, Shyam S.; Kamra, Devki N.; Sastry, Vadali R. B.
  • Archives of Animal Nutrition, Vol. 64, Issue 4
  • DOI: 10.1080/17450391003625037

Driving biomass breakdown through engineered cellulosomes
journal, February 2015

Biochemical and Microbiological Evidence for Fermentative Digestion in Free‐Living Land Iguanas ( Conolophus pallidus ) and Marine Iguanas ( Amblyrhynchus cristatus ) on the Galápagos Archipelago
journal, January 2004

  • Mackie, Roderick I.; Rycyk, Mathew; Ruemmler, Rebecca L.
  • Physiological and Biochemical Zoology, Vol. 77, Issue 1
  • DOI: 10.1086/383498

Reference databases for taxonomic assignment in metagenomics
journal, July 2012

  • Santamaria, M.; Fosso, B.; Consiglio, A.
  • Briefings in Bioinformatics, Vol. 13, Issue 6
  • DOI: 10.1093/bib/bbs036

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments
journal, August 2008

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
journal, June 2015

GenBank
journal, November 2012

  • Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1195

MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis
journal, May 2000

  • Fell, J. W.; Boekhout, T.; Fonseca, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 3
  • DOI: 10.1099/00207713-50-3-1351

Description of two anaerobic fungal strains from the bovine rumen and influence of diet on the fungal population in vivo
journal, July 1991

  • Kostyukovsky, V. A.; Okunev, O. N.; Tarakanov, B. V.
  • Journal of General Microbiology, Vol. 137, Issue 7
  • DOI: 10.1099/00221287-137-7-1759

Distribution of anaerobic fungi in the digestive tract of cattle and their survival in faeces
journal, June 1993

  • Davies, D. R.; Theodorou, M. K.; Lawrence, M. I. G.
  • Journal of General Microbiology, Vol. 139, Issue 6
  • DOI: 10.1099/00221287-139-6-1395

Presence in rumen bacterial and protozoal populations of enzymes capable of degrading fungal cell walls
journal, March 1994

Primary sequence and enzymic properties of two modular endoglucanases, Cel5A and Cel45A, from the anaerobic fungus Piromyces equi
journal, August 2000

Studies on the Rumen Flagellate Neocallimastix frontalis
journal, December 1975

Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome
journal, January 2005

Differential expression in RNA-seq: A matter of depth
journal, September 2011

  • Tarazona, S.; Garcia-Alcalde, F.; Dopazo, J.
  • Genome Research, Vol. 21, Issue 12
  • DOI: 10.1101/gr.124321.111

Anaerobic fungi (phylum Neocallimastigomycota ): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential
journal, August 2014

  • Gruninger, Robert J.; Puniya, Anil K.; Callaghan, Tony M.
  • FEMS Microbiology Ecology, Vol. 90, Issue 1
  • DOI: 10.1111/1574-6941.12383

Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin
journal, August 1992

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi: Methods
journal, March 2005

The UNITE database for molecular identification of fungi - recent updates and future perspectives: Letters
journal, March 2010

Interactions between rumen anaerobic fungi and ciliate protozoa in the degradation of rice straw cell walls
journal, January 1995

The survival of anaerobic fungi in cattle faeces
journal, July 1999

Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen: Initial colonization of forage by ruminal anaerobic fungi
journal, December 2008

The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages
journal, January 2015

  • Lee, S. M.; Guan, L. L.; Eun, J. -S.
  • Journal of Applied Microbiology, Vol. 118, Issue 3
  • DOI: 10.1111/jam.12724

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
journal, January 2011

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle
journal, February 2017

  • Li, Fuyong; Guan, Le Luo
  • Applied and Environmental Microbiology, Vol. 83, Issue 9
  • DOI: 10.1128/aem.00061-17

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen
journal, December 2014

  • Dai, Xin; Tian, Yan; Li, Jinting
  • Applied and Environmental Microbiology, Vol. 81, Issue 4
  • DOI: 10.1128/aem.03682-14

Cellulose Fermentation by a Rumen Anaerobic Fungus in Both the Absence and the Presence of Rumen Methanogens
journal, January 1981

Fermentation of Cellulose to Methane and Carbon Dioxide by a Rumen Anaerobic Fungus in a Triculture with Methanobrevibacter sp. Strain RA1 and Methanosarcina barkeri
journal, January 1982

  • Mountfort, Douglas O.; Asher, Rodney A.; Bauchop, Thomas
  • Applied and Environmental Microbiology, Vol. 44, Issue 1
  • DOI: 10.1128/aem.44.1.128-134.1982

Fermentation products and plant cell wall-degrading enzymes produced by monocentric and polycentric anaerobic ruminal fungi.
journal, January 1989

Influence of hydrogen-consuming bacteria on cellulose degradation by anaerobic fungi.
journal, January 1990

Effects of ruminal protozoa on cellulose degradation and the growth of an anaerobic ruminal fungus, Piromyces sp. strain OTS1, in vitro.
journal, January 1994

Cyllamyces aberensis gen.nov. sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle
journal, June 2001

  • Ozkose, Emin; Thomas, Barry J.; Davies, David R.
  • Canadian Journal of Botany, Vol. 79, Issue 6
  • DOI: 10.1139/b01-047

Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases
journal, July 2011

  • Wang, Pan; Qi,   Meng; Barboza,   Perry
  • Canadian Journal of Microbiology, Vol. 57, Issue 7
  • DOI: 10.1139/w11-048

Characterizing and measuring bias in sequence data
journal, January 2013

Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A
journal, December 2015

  • Couger, M. B.; Youssef, Noha H.; Struchtemeyer, Christopher G.
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0390-0

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
journal, February 2011

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach
journal, May 2011

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci
journal, June 2012

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities
journal, September 2013

Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows
journal, November 2013

The Role of Ciliate Protozoa in the Rumen
journal, November 2015

  • Newbold, Charles J.; de la Fuente, Gabriel; Belanche, Alejandro
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.01313

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches
journal, June 2016

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet
journal, January 2017

  • Comtet-Marre, Sophie; Parisot, Nicolas; Lepercq, Pascale
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.00067

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)
journal, October 2016

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces
journal, March 2015

The Rumen Ecosystem : As a Fountain Sources of Nobel Enzymes - Review -
journal, June 1999

  • Lee, S. S.; Shin, K. J.; Kim, W. Y.
  • Asian-Australasian Journal of Animal Sciences, Vol. 12, Issue 6
  • DOI: 10.5713/ajas.1999.988

Influence of an Anaerobic Fungal Culture (Orpinomyces sp.) Administration on Growth Rate, Ruminal Fermentation and Nutrient Digestion in Calves
journal, January 2004

  • Dey, Avijit; Sehgal, Jatinder Paul; Puniya, Anil Kumar
  • Asian-Australasian Journal of Animal Sciences, Vol. 17, Issue 6
  • DOI: 10.5713/ajas.2004.820
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Anaerobic Fungi in Gorilla (Gorilla gorilla gorilla) Feces: an Adaptation to a High-Fiber Diet?
    journal, July 2018

    • Schulz, Doreen; Qablan, Moneeb A.; Profousova-Psenkova, Ilona
    • International Journal of Primatology, Vol. 39, Issue 4
    • DOI: 10.1007/s10764-018-0052-8

    Review: The application of omics to rumen microbiota function
    journal, September 2018

    Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host
    journal, February 2020

    Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
    journal, September 2018

    • Huws, Sharon A.; Creevey, Christopher J.; Oyama, Linda B.
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.02161

    Metatranscriptomics reveals mycoviral populations in the ovine rumen
    journal, July 2019

    • Hitch, Thomas C. A.; Edwards, Joan E.; Gilbert, Rosalind A.
    • FEMS Microbiology Letters, Vol. 366, Issue 13
    • DOI: 10.1093/femsle/fnz161

    FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    journal, February 2018

    • Comtet-Marre, Sophie; Chaucheyras-Durand, Frédérique; Bouzid, Ourdia
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.00215

    A Multi-Kingdom Study Reveals the Plasticity of the Rumen Microbiota in Response to a Shift From Non-grazing to Grazing Diets in Sheep
    journal, February 2019

    • Belanche, Alejandro; Kingston-Smith, Alison H.; Griffith, Gareth W.
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.00122

    Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis
    journal, October 2019

    • Edwards, Joan E.; Hermes, Gerben D. A.; Kittelmann, Sandra
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.02370

    Liebetanzomyces polymorphus gen. et sp. nov., a new anaerobic fungus (Neocallimastigomycota) isolated from the rumen of a goat
    journal, October 2018

    Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
    journal, September 2020

    Maternal versus artificial rearing shapes the rumen microbiome having minor long‐term physiological implications
    journal, October 2019

    • Belanche, Alejandro; Yáñez‐Ruiz, David R.; Detheridge, Andrew P.
    • Environmental Microbiology, Vol. 21, Issue 11
    • DOI: 10.1111/1462-2920.14801

    FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota
    journal, February 2018

    • Comtet-Marre, Sophie; Chaucheyras-Durand, Frédérique; Bouzid, Ourdia
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.00215
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: