skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this work briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. Finally, we also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.

Authors:
 [1];  [1];  [1];  [2];  [1]
  1. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering
  2. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering; Harper Adams Univ., Newport (United Kingdom). Animal Production, Welfare, and Veterinary 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) (SC-23); United States Dept. of Agriculture (USDA); US Army Research Office (ARO)
OSTI Identifier:
1485183
Grant/Contract Number:  
SC0010352; 2011-67017-20459
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology and Bioengineering
Additional Journal Information:
Journal Volume: 111; Journal Issue: 8; Journal ID: ISSN 0006-3592
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anaerobic fungi; cellulase; cellulosome; biofuels; hydrogenosome

Citation Formats

Haitjema, Charles H., Solomon, Kevin V., Henske, John K., Theodorou, Michael K., and O'Malley, Michelle A. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. United States: N. p., 2014. Web. doi:10.1002/bit.25264.
Haitjema, Charles H., Solomon, Kevin V., Henske, John K., Theodorou, Michael K., & O'Malley, Michelle A. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. United States. doi:10.1002/bit.25264.
Haitjema, Charles H., Solomon, Kevin V., Henske, John K., Theodorou, Michael K., and O'Malley, Michelle A. Thu . "Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production". United States. doi:10.1002/bit.25264. https://www.osti.gov/servlets/purl/1485183.
@article{osti_1485183,
title = {Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production},
author = {Haitjema, Charles H. and Solomon, Kevin V. and Henske, John K. and Theodorou, Michael K. and O'Malley, Michelle A.},
abstractNote = {Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this work briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. Finally, we also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.},
doi = {10.1002/bit.25264},
journal = {Biotechnology and Bioengineering},
issn = {0006-3592},
number = 8,
volume = 111,
place = {United States},
year = {2014},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
journal, February 2013


A rapid DNA isolation procedure applicable to many refractory filamentous fungi
journal, January 1988


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


Enzyme-based DNA extraction from zoospores of ruminal fungi
journal, January 1992


Xylanases of anaerobic fungus Anaeromyces mucronatus
journal, July 2010


Caecomyces sympodialis sp. nov., a new rumen fungus isolated from Bos indicus
journal, January 2007


Studies on the Rumen Flagellate Neocallimastix frontalis
journal, December 1975


Characterization of a Double Dockerin from the Cellulosome of the Anaerobic Fungus Piromyces equi
journal, October 2007

  • Nagy, Tibor; Tunnicliffe, Richard B.; Higgins, Lee D.
  • Journal of Molecular Biology, Vol. 373, Issue 3
  • DOI: 10.1016/j.jmb.2007.08.007

Determination of growth of anaerobic fungi on soluble and cellulosic substrates using a pressure transducer
journal, March 1995


Assembly of Minicellulosomes on the Surface of Bacillus subtilis
journal, May 2011

  • Anderson, Timothy D.; Robson, Scott A.; Jiang, Xiao Wen
  • Applied and Environmental Microbiology, Vol. 77, Issue 14
  • DOI: 10.1128/AEM.02599-10

Substrate binding of a GH5 endoglucanase from the ruminal fungus Piromyces rhizinflata
journal, September 2011

  • Tseng, Chih-Wen; Ko, Tzu-Ping; Guo, Rey-Ting
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 10
  • DOI: 10.1107/S1744309111032428

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


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

Simple method for cryopreservation of an anaerobic rumen fungus using ethylene glycol and rumen fluid
journal, April 1995


Survival of anaerobic fungus Caecomyces sp. in various preservation methods: a comparative study
journal, November 2012


The Rumen Flagellate Piromonas communis: Its Life-history and Invasion of Plant Material in the Rumen
journal, March 1977


An intron-containing glycoside hydrolase family 9 cellulase gene encodes the dominant 90 kDa component of the cellulosome of the anaerobic fungus Piromyces sp. strain E2
journal, July 2002

  • Steenbakkers, Peter J. M.; Ubhayasekera, Wimal; Goossen, Harry J. A. M.
  • Biochemical Journal, Vol. 365, Issue 1
  • DOI: 10.1042/bj20011866

Structural modeling and further improvement in pH stability and activity of a highly-active xylanase from an uncultured rumen fungus
journal, November 2012


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


Functional Display of Complex Cellulosomes on the Yeast Surface via Adaptive Assembly
journal, July 2012

  • Tsai, Shen-Long; DaSilva, Nancy A.; Chen, Wilfred
  • ACS Synthetic Biology, Vol. 2, Issue 1
  • DOI: 10.1021/sb300047u

Degradation of leaf blades and stems by monocentric and polycentric isolates of ruminal fungi
journal, December 1990


Transient expression of the β-glucuronidase gene after biolistic transformation of the anaerobic fungus Neocallimastix frontalis
journal, February 1997


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


InterPro in 2011: new developments in the family and domain prediction database
journal, November 2011

  • Hunter, S.; Jones, P.; Mitchell, A.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr948

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

The Major Component of the Cellulosomes of Anaerobic Fungi from the Genus Piromyces is a Family 48 Glycoside Hydrolase
journal, January 2002


Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

Cellulosomes: Highly Efficient Nanomachines Designed to Deconstruct Plant Cell Wall Complex Carbohydrates
journal, June 2010


Noncatalytic Docking Domains of Cellulosomes of Anaerobic Fungi
journal, September 2001


Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
journal, January 2010


Cellulases and hemicellulases of the anaerobic fungus Piromyces constitute a multiprotein cellulose-binding complex and are encoded by multigene families
journal, January 1995


Studies on the capacity of the cellulase of the anaerobic rumen fungus Piromonas communis P to degrade hydrogen bond-ordered cellulose
journal, July 1995

  • Wood, T. M.; Wilson, C. A.
  • Applied Microbiology and Biotechnology, Vol. 43, Issue 3
  • DOI: 10.1007/BF00218468

Evaluating expression and catalytic activity of anaerobic fungal fibrolytic enzymes native topiromyces sp E2 inSaccharomyces cerevisiae
journal, December 2011

  • O'Malley, Michelle A.; Theodorou, Michael K.; Kaiser, Chris A.
  • Environmental Progress & Sustainable Energy, Vol. 31, Issue 1
  • DOI: 10.1002/ep.10614

A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5
journal, January 2012

  • Chen, Hsin-Liang; Chen, Yo-Chia; Lu, Mei-Yeh
  • Biotechnology for Biofuels, Vol. 5, Issue 1
  • DOI: 10.1186/1754-6834-5-24

GeneMark.hmm: new solutions for gene finding
journal, February 1998


Remarkably AT-rich genomic DNA from the anaerobic fungus Neocallimastix
journal, January 1989


Cheap third-generation sequencing
journal, April 2009


Hydrogenosomes in the rumen fungus Neocallimastix patriciarum
journal, June 1986

  • Yarlett, N.; Orpin, C. G.; Munn, E. A.
  • Biochemical Journal, Vol. 236, Issue 3
  • DOI: 10.1042/bj2360729

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

Xylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway
journal, June 2003

  • Harhangi, Harry R.; Akhmanova, Anna S.; Emmens, Roul
  • Archives of Microbiology, Vol. 180, Issue 2
  • DOI: 10.1007/s00203-003-0565-0

A Model to Interpret Gas Accumulation Profiles Associated with In Vitro Degradation of Ruminant Feeds
journal, July 1993

  • France, J.; Dhanoa, M. S.; Theodorou, M. K.
  • Journal of Theoretical Biology, Vol. 163, Issue 1
  • DOI: 10.1006/jtbi.1993.1109

A highly expressed family 1 β-glucosidase with transglycosylation capacity from the anaerobic fungus Piromyces sp. E2
journal, April 2002

  • Harhangi, Harry R.; Steenbakkers, Peter J. M.; Akhmanova, Anna
  • Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, Vol. 1574, Issue 3
  • DOI: 10.1016/S0167-4781(01)00380-3

Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms
journal, October 2000


Characterization of hydrogenosomes and their role in glucose metabolism of Neocallimastix sp. L2
journal, November 1993

  • Marvin-Sikkema, FemkeD.; Pedro Gomes, TeresaM.; Grivet, Jean-Philippe
  • Archives of Microbiology, Vol. 160, Issue 5
  • DOI: 10.1007/BF00252226

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

Enhanced cellulose degradation by targeted integration of a cohesin-fused  -glucosidase into the Clostridium thermocellum cellulosome
journal, June 2012

  • Gefen, G.; Anbar, M.; Morag, E.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 26
  • DOI: 10.1073/pnas.1202747109

Fermentation of cellulose and production of cellulolytic and xylanolytic enzymes by anaerobic fungi from ruminant and non-ruminant herbivores
journal, September 1991

  • Teunissen, M. J.; Smits, A. A. M.; Op den Camp, H. J. M.
  • Archives of Microbiology, Vol. 156, Issue 4
  • DOI: 10.1007/BF00263000

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
journal, January 2011

  • Wang, Tzi-Yuan; Chen, Hsin-Liang; Lu, Mei-Yeh J.
  • Biotechnology for Biofuels, Vol. 4, Issue 1
  • DOI: 10.1186/1754-6834-4-24

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

A novel hybrid gene prediction method employing protein multiple sequence alignments
journal, January 2011


Review Article: The hydrogenosome
journal, December 1993


Studies on the Rumen Flagellate Sphaeromonas communis
journal, June 1976


Identification of spores in the polycentric anaerobic gut fungi which enhance their ability to survive
journal, March 2000


Next-generation DNA sequencing
journal, October 2008

  • Shendure, Jay; Ji, Hanlee
  • Nature Biotechnology, Vol. 26, Issue 10
  • DOI: 10.1038/nbt1486

Molecular cloning and characterization of a β-glucanase from Piromyces rhizinflatus
journal, May 2011

  • Chu, Chih-Yuan; Tseng, Chih-Wen; Yueh, Pei-Ying
  • Journal of Bioscience and Bioengineering, Vol. 111, Issue 5
  • DOI: 10.1016/j.jbiosc.2011.01.009

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

Classification of Anaerobic Gut Fungi from Herbivores with Emphasis on Rumen Fungi from Malaysia
journal, September 1995

  • Ho, Y. W.; Barr, D. J. S.
  • Mycologia, Vol. 87, Issue 5
  • DOI: 10.2307/3760810

NCBI BLAST: a better web interface
journal, May 2008

  • Johnson, M.; Zaretskaya, I.; Raytselis, Y.
  • Nucleic Acids Research, Vol. 36, Issue Web Server
  • DOI: 10.1093/nar/gkn201

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations
journal, July 2003

  • Dressman, D.; Yan, H.; Traverso, G.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 15, p. 8817-8822
  • DOI: 10.1073/pnas.1133470100

Characterization of an anaerobic fungus from Ilama faeces
journal, October 1992


Cellulosic ethanol production using a yeast consortium displaying a minicellulosome and β-glucosidase
journal, January 2013


RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
journal, August 2011


The role of the cellulolytic high molecular mass (HMM) complex of the anaerobic fungus Piromyces sp. strain E2 in the hydrolysis of microcrystalline cellulose
journal, March 1997

  • Dijkerman, R.; Op den Camp, Huub J. M.; Van der Drift, Chris
  • Archives of Microbiology, Vol. 167, Issue 2-3
  • DOI: 10.1007/s002030050426

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


The Billion-Ton Biofuels Vision
journal, June 2006


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


Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing
journal, August 2014


Commentary on the Hungate technique for culture of anaerobic bacteria
journal, December 1972


Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
journal, January 2008

  • Nilsson, R. Henrik; Kristiansson, Erik; Ryberg, Martin
  • Evolutionary Bioinformatics, Vol. 4
  • DOI: 10.4137/EBO.S653

    Works referencing / citing this record:

    Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters
    journal, December 2016

    • Seppälä, Susanna; Solomon, Kevin V.; Gilmore, Sean P.
    • Microbial Cell Factories, Vol. 15, Issue 1
    • DOI: 10.1186/s12934-016-0611-7

    Engineering a highly active thermophilic β-glucosidase to enhance its pH stability and saccharification performance
    journal, July 2016


    Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation
    journal, April 2018

    • Hartinger, Thomas; Gresner, Nina; Südekum, Karl-Heinz
    • Journal of Animal Science and Biotechnology, Vol. 9, Issue 1
    • DOI: 10.1186/s40104-018-0249-x