[1] DEARING M D, KOHL K D.Beyond fermentation:other important services provided to endothermic herbivores by their gut microbiota[J].Integrative and Comparative Biology, 2017, 57(4):723-731.
[2] MORGAVI D P, KELLY W J, JANSSEN P H, et al.Rumen microbial (meta) genomics and its application to ruminant production[J].Animal, 2013, 7(Suppl.1):184-201.
[3] DEHORITY B A.Gastrointestinal tracts of herbivores, particularly the ruminant:anatomy, physiology and microbial digestion of plants[J].Journal of Applied Animal Research, 2002, 21(2):145-160.
[4] GRUNINGER R J, PUNIYA A K, CALLAGHAN T M, et al.Anaerobic fungi (phylum Neocallimastigomycota):advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential[J].FEMS Microbiology Ecology, 2014, 90(1):1-17.
[5] JENSEN E A, HAMMOND D M.A morphological study of trichomonads and related flagellates from the bovine digestive tract[J].The Journal of Protozoology, 1964, 11(3):386-394.
[6] ORPIN C G.Studies on the rumen flagellate
Neocallimastix frontalis[J].Journal of General Microbiology, 1975, 91(2):249-262.
[7] ORPIN C G.The rumen flagellate
Piromonas communis:its life-history and invasion of plant material in the rumen[J].Journal of General Microbiology, 1977, 99(1):107-117.
[8] BARR D J S.An outline for the reclassification of the
Chytridiales, and for a new order, the Spizellomycetales[J].Canadian Journal of Botany, 1980, 58(22):2380-2394.
[9] DORE J, STAHL D A.Phylogeny of anaerobic rumen Chytridiomycetes inferred from small subunit ribosomal RNA sequence comparisons[J].Canadian Journal of Botany, 1991, 69(9):1964-1971.
[10] LI J L, HEATH I B, PACKER L.The phylogenetic relationships of the anaerobic chytridiomycetous gut fungi (Neocallimasticaceae) and the Chytridiomycota.Ⅱ.Cladistic analysis of structural data and description of Neocallimasticales ord.nov.[J].Canadian Journal of Botany, 1993, 71(3):393-407.
[11] JAMES T Y, KAUFF F, SCHOCH C L, et al.Reconstructing the early evolution of fungi using a six-gene phylogeny[J].Nature, 2006, 443(7113):818-822.
[12] HIBBETT D S, BINDER M, BISCHOFF J F, et al.A higher-level phylogenetic classification of the fungi[J].Mycological Research, 2007, 111(Pt 5):509-547.
[13] SCHOCH C L, SEIFERT K A, HUHNDORF S, et al.Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi[J].Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(16):6241-6246.
[14] EBERSBERGER I, DE MATOS SIMOES R, KUPCZOK A, et al.A consistent phylogenetic backbone for the fungi[J].Molecular Biology and Evolution, 2012, 29(5):1319-1334.
[15] TEDERSOO L, SÁNCHEZ-RAMÍREZ S, KÕLJALG U, et al.High-level classification of the Fungi and a tool for evolutionary ecological analyses[J].Fungal Diversity, 2018, 90(1):135-159.
[16] WANG Y, YOUSSEF N H, COUGER M B, et al.Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes[J].mSystems, 2019, 4(4):e00247-19.
[17] HESS M, PAUL S S, PUNIYA A K, et al.Anaerobic fungi:past, present, and future[J].Frontiers in Microbiology, 2020, 11:584893.
[18] EDWARDS J E, FORSTER R J, CALLAGHAN T M, et al.PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi:insights, challenges and opportunities[J].Frontiers in Microbiology, 2017, 8:1657.
[19] DOLLHOFER V, CALLAGHAN T M, DORN-IN S, et al.Development of three specific PCR-based tools to determine quantity, cellulolytic transcriptional activity and phylogeny of anaerobic fungi[J].Journal of Microbiological Methods, 2016, 127:28-40.
[20] ZHANG Y W, LI F Y, CHEN Y H, et al.Metatranscriptomic profiling reveals the effect of breed on active rumen eukaryotic composition in beef cattle with varied feed efficiency[J].Frontiers in Microbiology, 2020, 11:367.
[21] KITTELMANN S, NAYLOR G E, KOOLAARD J P, et al.A proposed taxonomy of anaerobic fungi (class Neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis[J].PLoS One, 2012, 7(5):e36866.
[22] DAGAR S S, KUMAR S, GRIFFITH G W, et al.A new anaerobic fungus (
Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (
Camelus dromedarius)[J].Fungal Biology, 2015, 119(8):731-737.
[23] CALLAGHAN T M, PODMIRSEG S M, HOHLWECK D, et al.
Buwchfawromyces eastonii gen. nov., sp. nov.:a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces[J].MycoKeys, 2015, 9:11-28.
[24] PAUL S S, BU D P, XU J C, et al.A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework[J].Fungal Diversity, 2018, 89(1):253-266.
[25] LIGGENSTOFFER A S, YOUSSEF N H, COUGER M B, et al.Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores[J].The ISME Journal, 2010, 4(10):1225-1235.
[26] KOETSCHAN C, KITTELMANN S, LU J L, et al.Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota)[J].PLoS One, 2014, 9(3):e91928.
[27] BENSON D A, CAVANAUGH M, CLARK K, et al.GenBank[J].Nucleic Acids Research, 2013, 41(Database Issue):D36-D42.
[28] KÕLJALG U, NILSSON R H, ABARENKOV K, et al.Towards a unified paradigm for sequence-based identification of fungi[J].Molecular Ecology, 2013, 22(21):5271-5277.
[29] SANTAMARIA M, FOSSO B, CONSIGLIO A, et al.Reference databases for taxonomic assignment in metagenomics[J].Briefings in Bioinformatics, 2012, 13(6):682-695.
[30] MAHÉ S, DUHAMEL M, LE CALVEZ T, et al.PHYMYCO-DB:a curated database for analyses of fungal diversity and evolution[J].PLoS One, 2012, 7(9):e43117.
[31] TUCKWELL D S, NICHOLSON M J, MCSWEENEY C S, et al.The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints[J].Microbiology, 2005, 151(Pt 5):1557-1567.
[32] KELLER A, FÖRSTER F, MVLLER T, et al.Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees[J].Biology Direct, 2010, 5:4.
[33] HANAFY R A, ELSHAHED M S, YOUSSEF N H.
Feramyces austinii, gen. nov., sp. nov., an anaerobic gut fungus from rumen and fecal samples of wild Barbary sheep and fallow deer[J].Mycologia, 2018, 110(3):513-525.
[34] JOSHI A, LANJEKAR V B, DHAKEPHALKAR P K, et al.
Liebetanzomycespolymorphus gen. et sp. nov., a new anaerobic fungus (Neocallimastigomycota) isolated from the rumen of a goat[J].MycoKeys, 2018, 40:89-110.
[35] STABEL M, HANAFY R A, SCHWEITZER T, et al.
Aestipascuomyces dupliciliberans gen. nov, sp. nov., the first cultured representative of the uncultured SK4 clade from aoudad sheep and alpaca[J].Microorganisms, 2020, 8(11):1734.
[36] HANAFY R A, LANJEKAR V B, DHAKEPHALKAR P K, et al.Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum[J].Mycologia, 2020, 112(6):1212-1239.
[37] EDWARDS J E, KINGSTON-SMITH A H, JIMENEZ H R, et al.Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen[J].FEMS Microbiology Ecology, 2008, 66(3):537-545.
[38] EDWARDS J E, HERMES G D A, KITTELMANN S, et al.Assessment of the accuracy of high-throughput sequencing of the ITS1 region of Neocallimastigomycota for community composition analysis[J].Frontiers in Microbiology, 2019, 10:2370.
[39] DAGAR S S, KUMAR S, MUDGIL P, et al.D1/D2 domain of large-subunit ribosomal DNA for differentiation of
Orpinomyces spp[J].Applied and Environmental Microbiology, 2011, 77(18):6722-6725.
[40] DETHERIDGE A P, BRAND G, FYCHAN R, et al.The legacy effect of cover crops on soil fungal populations in a cereal rotation[J].Agriculture Ecosystems & Environment, 2016, 228:49-61.
[41] WANG X W, LIU X Z, GROENEWALD J Z.Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China[J].Antonie Van Leeuwenhoek, 2017, 110(1):87-103.
[42] HAUSNER G, INGLIS G D, YANKE L J, et al.Analysis of restriction fragment length polymorphisms in the ribosomal DNA of a selection of anaerobic chytrids[J].Canadian Journal of Botany, 2000, 78(7):917-927.
[43] FLIEGEROVA K, MRAZEK J, VOIGT K.Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP[J].Folia Microbiologica, 2006, 51(4):273-277.
[44] HANAFY R A, ELSHAHED M S, LIGGENSTOFFER A S, et al.
Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep[J].Mycologia, 2017, 109(2):231-243.
[45] NAGLER M, PODMIRSEG S M, GRIFFITH G W, et al.The use of extracellular DNA as a proxy for specific microbial activity[J].Applied Microbiology and Biotechnology, 2018, 102(6):2885-2898.
[46] DOLLHOFER V, CALLAGHAN T M, GRIFFITH G W, et al.Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants[J].Bioresource Technology, 2017, 235:131-139.
[47] NAGLER M, KOZJEK K, ETEMADI M, et al.Simple yet effective:microbial and biotechnological benefits of rumen liquid addition to lignocellulose-degrading biogas plants[J].Journal of Biotechnology, 2019, 300:1-10.
[48] WURZBACHER C, LARSSON E, BENGTSSON-PALME J, et al.Introducing ribosomal tandem repeat barcoding for fungi[J].Molecular Ecology Resources, 2019, 19(1):118-127.
[49] HANAFY R A, JOHNSON B, YOUSSEF N H, et al.Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation[J].Environmental Microbiology, 2020, 22(9):3883-3908.
[50] HEATH I B, BAUCHOP T, SKIPP R A.Assignment of the rumen anaerobe
Neocallimastix frontalis to the Spizellomycetales (Chytridiomycetes) on the basis of its polyflagellate zoospore ultrastructure[J].Canadian Journal of Botany, 1983, 61(1):295-307.
[51] BARR D J S, KUDO H, JAKOBER K D, et al.Morphology and development of rumen fungi:
Neocallimastix sp.,
Piromyces communis, and
Orpinomyces bovis gen.nov., sp.nov.[J].Canadian Journal of Botany, 1989, 67(9):2815-2824.
[52] BRETON A, BERNALIER A, DUSSER M, et al.
Anaeromyces mucronatus nov. gen., nov. sp.A new strictly anaerobic rumen fungus with polycentric thallus[J].FEMS Microbiology Letters, 1990, 58(2):177-182.
[53] GOLD J J, HEATH I B, BAUCHOP T.Ultrastructural description of a new chytrid genus of caecum anaerobe,
Caecomyces equi gen. nov., sp. nov., assigned to the
Neocallimasticaceae[J].Bio Systems, 1988, 21(3/4):403-415.
[54] OZKOSE E, THOMAS B J, DAVIES D R, et al.
Cyllamyces aberensis gen.nov.sp.nov., a new anaerobic gut fungus with branched sporangiophores isolated from cattle[J].Canadian Journal of Botany, 2001, 79(6):666-673.
