Solomon KV, Henske JK, Theodorou MK, O’Malley MA
(2016b) Robust and effective methodologies for
cryopreservation and DNA extraction from anaerobic gut fungi. Anaerobe 38:39–46. https://doi.org/
10.1016/j.anaerobe.2015.11.008
Solomon KV, Henske JK, Gilmore SP, Lipzen A, Grigoriev IV, Thompson D, O’Malley MA (2018) Catabolic repression in early-diverging anaerobic fungi
is partially mediated by natural antisense transcripts. Fungal Genet Biol 121:1–9. https://doi.
org/10.1016/j.fgb.2018.09.004
Strauss J, Mach RL, Zeilinger S, Hartler G, Sto ¨ffler G,
Wolschek M, Kubicek CP (1995) Crel, the carbon
catabolite repressor protein from Trichoderma
reesei. FEBS Lett 376 (1):103–107. https://doi.org/
10.1016/0014-5793(95)01255-5
Strzalka R, Schneider D, Eicker U (2017) Current status
of bioenergy technologies in Germany. Renew Sustain Energy Rev 72:801–820. https://doi.org/
10.1016/j.rser.2017.01.091
Swift CL, Brown JL, Seppa ¨la ¨ S, O’Malley MA (2019) Cocultivation of the anaerobic fungus Anaeromyces
robustus with Methanobacterium bryantii
enhances transcription of carbohydrate active
enzymes. J Ind Microbiol Biotechnol. https://doi.
org/10.1007/s10295-019-02188-0
Ter Beek J, Guskov A, Slotboom DJ (2014) Structural
diversity of ABC transporters. J Gen Physiol 143
(4):419–435.
https://doi.org/10.1085/
jgp.201411164
Teunissen MJ, Baerends RJS, Knelissen RAG, Op den
Camp HJM, Vogels GD (1992) A semi-continuous
culture system for production of cellulolytic and
xylanolytic enzymes by the anaerobic fungus Piromyces sp. strain E2. Appl Microbiol Biotechnol 38
(1):28–33. https://doi.org/10.1007/bf00169414
Theodorou MK, Gill M, King-Spooner C, Beever DE
(1990) Enumeration of anaerobic chytridiomycetes as thallus-forming units: novel method for
quantification of fibrolytic fungal populations
from the digestive tract ecosystem. Appl Environ
Microbiol 56(4):1073–1078. http://aem.asm.org/
content/56/4/1073.full.pdf
Theodorou MK, Mennim G, Davies DR, Zhu WY, Trinci
AP, Brookman JL (1996a) Anaerobic fungi in the
digestive tract of mammalian herbivores and their
potential for exploitation. Proc Nutr Soc 55
(3):913–926. https://doi.org/10.1079/pns19960088
Theodorou MK, Zhu W-Y, Rickers A, Nielsen BB, Gull
K, Trinci APJ (1996b) Biochemistry and ecology of
anaerobic fungi. In: Howard DH, Miller JD (eds)
Human and animal relationships. Springer, Berlin,
pp 265–295. https://doi.org/10.1007/978-3-66210373-9_14
Trinci APG, Davies DR, Gull K, Lawrence MI, Nielsen
BB, Rickers A (1994) Anaerobic fungi in herbivorous animals. Mycol Res 98. https://doi.org/
10.1016/s0953-7562(09)80178-0
Tripathi VK, Sehgal JP, Puniya AK, Singh K (2007)
Effect of administration of anaerobic fungi
isolated from cattle and wild blue bull (Boselaphus
tragocamelus) on growth rate and fibre utilization
in buffalo calves AU - Tripathi, Vimal K. Arch
Anim Nutr 61(5):416–423. https://doi.org/
10.1080/17450390701556759
Tsai C-F, Qiu X, Liu J-H (2003) A comparative analysis
of two cDNA clones of the cellulase gene family
from anaerobic fungus Piromyces rhizinflata.
Anaerobe 9(3):131–140. https://doi.org/10.1016/
S1075-9964(03)00087-8
Ushida K, Newbold CJ, Jouany JP (1997) Interspecies
hydrogen transfer between the rumen ciliate Polyplastron multivesiculatum and Methanosarcina
barkeri. J Gen Appl Microbiol 43(2):129–131.
https://www.ncbi.nlm.nih.gov/pubmed/12501346
van der Giezen M, Kiel JAKW, Sjollema KA, Prins RA
(1998) The hydrogenosomal malic enzyme from
the anaerobic fungus Neocallimastix frontalis is
targeted to mitochondria of the methylotrophic
yeast Hansenula polymorpha. Curr Genet 33
(2):131–135.
https://doi.org/10.1007/
s002940050318
Wang T-Y, Chen H-L, Lu M-Y, Chen Y-C, Sung H-M,
Mao C-T, Cho H-Y, Ke H-M, Hwa T-Y, Ruan S-K,
Hung K-Y, Chen C-K, Li J-Y, Wu Y-C, Chen Y-H,
Chou S-P, Tsai Y-W, Chu T-C, Shih C-C, Li W-H,
Shih M-C (2011) Functional characterization of
cellulases identified from the cow rumen fungus
Neocallimastix patriciarum W5 by transcriptomic
and secretomic analyses. Biotechnol Biofuels 4
(1):24. https://doi.org/10.1186/1754-6834-4-24
Wang X, Liu X, Groenewald JZ (2017) Phylogeny of
anaerobic fungi (phylum Neocallimastigomycota),
with contributions from yak in China. Antonie
Van Leeuwenhoek 110(1):87–103. https://doi.org/
10.1007/s10482-016-0779-1
Wang Y, Youssef N, Couger M, Hanafy R, Elshahed M,
Stajich JE (2019) Comparative genomics and
divergence time estimation of the anaerobic fungi
in herbivorous mammals. bioRxiv 401869 [Preprint]. 31 Aug 2018 [cited 30 Mar 2019]. Available
from https://doi.org/10.1101/401869
Weimer PJ, Russell JB, Muck RE (2009) Lessons from
the cow: what the ruminant animal can teach us
about consolidated bioprocessing of cellulosic biomass. Bioresour Technol 100(21):5323–5331.
https://doi.org/10.1016/j.biortech.2009.04.075
Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppa ¨la ¨ S, O’Malley MA (2019) Linking ‘omics’ to
function unlocks the biotech potential of nonmodel fungi. Curr Opin Syst Biol 14:9–17..
https://doi.org/10.1016/j.coisb.2019.02.001
Wilson CA, Wood TM (1992) The anaerobic fungus
Neocallimastix frontalis: isolation and properties
of a cellulosome-type enzyme fraction with the
capacity to solubilize hydrogen-bond-ordered cellulose. Appl Microbiol Biotechnol 37(1):125–129.
436
V. Flad et al.
(2016b) Robust and effective methodologies for
cryopreservation and DNA extraction from anaerobic gut fungi. Anaerobe 38:39–46. https://doi.org/
10.1016/j.anaerobe.2015.11.008
Solomon KV, Henske JK, Gilmore SP, Lipzen A, Grigoriev IV, Thompson D, O’Malley MA (2018) Catabolic repression in early-diverging anaerobic fungi
is partially mediated by natural antisense transcripts. Fungal Genet Biol 121:1–9. https://doi.
org/10.1016/j.fgb.2018.09.004
Strauss J, Mach RL, Zeilinger S, Hartler G, Sto ¨ffler G,
Wolschek M, Kubicek CP (1995) Crel, the carbon
catabolite repressor protein from Trichoderma
reesei. FEBS Lett 376 (1):103–107. https://doi.org/
10.1016/0014-5793(95)01255-5
Strzalka R, Schneider D, Eicker U (2017) Current status
of bioenergy technologies in Germany. Renew Sustain Energy Rev 72:801–820. https://doi.org/
10.1016/j.rser.2017.01.091
Swift CL, Brown JL, Seppa ¨la ¨ S, O’Malley MA (2019) Cocultivation of the anaerobic fungus Anaeromyces
robustus with Methanobacterium bryantii
enhances transcription of carbohydrate active
enzymes. J Ind Microbiol Biotechnol. https://doi.
org/10.1007/s10295-019-02188-0
Ter Beek J, Guskov A, Slotboom DJ (2014) Structural
diversity of ABC transporters. J Gen Physiol 143
(4):419–435.
https://doi.org/10.1085/
jgp.201411164
Teunissen MJ, Baerends RJS, Knelissen RAG, Op den
Camp HJM, Vogels GD (1992) A semi-continuous
culture system for production of cellulolytic and
xylanolytic enzymes by the anaerobic fungus Piromyces sp. strain E2. Appl Microbiol Biotechnol 38
(1):28–33. https://doi.org/10.1007/bf00169414
Theodorou MK, Gill M, King-Spooner C, Beever DE
(1990) Enumeration of anaerobic chytridiomycetes as thallus-forming units: novel method for
quantification of fibrolytic fungal populations
from the digestive tract ecosystem. Appl Environ
Microbiol 56(4):1073–1078. http://aem.asm.org/
content/56/4/1073.full.pdf
Theodorou MK, Mennim G, Davies DR, Zhu WY, Trinci
AP, Brookman JL (1996a) Anaerobic fungi in the
digestive tract of mammalian herbivores and their
potential for exploitation. Proc Nutr Soc 55
(3):913–926. https://doi.org/10.1079/pns19960088
Theodorou MK, Zhu W-Y, Rickers A, Nielsen BB, Gull
K, Trinci APJ (1996b) Biochemistry and ecology of
anaerobic fungi. In: Howard DH, Miller JD (eds)
Human and animal relationships. Springer, Berlin,
pp 265–295. https://doi.org/10.1007/978-3-66210373-9_14
Trinci APG, Davies DR, Gull K, Lawrence MI, Nielsen
BB, Rickers A (1994) Anaerobic fungi in herbivorous animals. Mycol Res 98. https://doi.org/
10.1016/s0953-7562(09)80178-0
Tripathi VK, Sehgal JP, Puniya AK, Singh K (2007)
Effect of administration of anaerobic fungi
isolated from cattle and wild blue bull (Boselaphus
tragocamelus) on growth rate and fibre utilization
in buffalo calves AU - Tripathi, Vimal K. Arch
Anim Nutr 61(5):416–423. https://doi.org/
10.1080/17450390701556759
Tsai C-F, Qiu X, Liu J-H (2003) A comparative analysis
of two cDNA clones of the cellulase gene family
from anaerobic fungus Piromyces rhizinflata.
Anaerobe 9(3):131–140. https://doi.org/10.1016/
S1075-9964(03)00087-8
Ushida K, Newbold CJ, Jouany JP (1997) Interspecies
hydrogen transfer between the rumen ciliate Polyplastron multivesiculatum and Methanosarcina
barkeri. J Gen Appl Microbiol 43(2):129–131.
https://www.ncbi.nlm.nih.gov/pubmed/12501346
van der Giezen M, Kiel JAKW, Sjollema KA, Prins RA
(1998) The hydrogenosomal malic enzyme from
the anaerobic fungus Neocallimastix frontalis is
targeted to mitochondria of the methylotrophic
yeast Hansenula polymorpha. Curr Genet 33
(2):131–135.
https://doi.org/10.1007/
s002940050318
Wang T-Y, Chen H-L, Lu M-Y, Chen Y-C, Sung H-M,
Mao C-T, Cho H-Y, Ke H-M, Hwa T-Y, Ruan S-K,
Hung K-Y, Chen C-K, Li J-Y, Wu Y-C, Chen Y-H,
Chou S-P, Tsai Y-W, Chu T-C, Shih C-C, Li W-H,
Shih M-C (2011) Functional characterization of
cellulases identified from the cow rumen fungus
Neocallimastix patriciarum W5 by transcriptomic
and secretomic analyses. Biotechnol Biofuels 4
(1):24. https://doi.org/10.1186/1754-6834-4-24
Wang X, Liu X, Groenewald JZ (2017) Phylogeny of
anaerobic fungi (phylum Neocallimastigomycota),
with contributions from yak in China. Antonie
Van Leeuwenhoek 110(1):87–103. https://doi.org/
10.1007/s10482-016-0779-1
Wang Y, Youssef N, Couger M, Hanafy R, Elshahed M,
Stajich JE (2019) Comparative genomics and
divergence time estimation of the anaerobic fungi
in herbivorous mammals. bioRxiv 401869 [Preprint]. 31 Aug 2018 [cited 30 Mar 2019]. Available
from https://doi.org/10.1101/401869
Weimer PJ, Russell JB, Muck RE (2009) Lessons from
the cow: what the ruminant animal can teach us
about consolidated bioprocessing of cellulosic biomass. Bioresour Technol 100(21):5323–5331.
https://doi.org/10.1016/j.biortech.2009.04.075
Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppa ¨la ¨ S, O’Malley MA (2019) Linking ‘omics’ to
function unlocks the biotech potential of nonmodel fungi. Curr Opin Syst Biol 14:9–17..
https://doi.org/10.1016/j.coisb.2019.02.001
Wilson CA, Wood TM (1992) The anaerobic fungus
Neocallimastix frontalis: isolation and properties
of a cellulosome-type enzyme fraction with the
capacity to solubilize hydrogen-bond-ordered cellulose. Appl Microbiol Biotechnol 37(1):125–129.
436
V. Flad et al.