This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

Área de Microbiología Facultad de Ciencias Médicas Universidad Nacional de Cuyo Mendoza M5500 Argentina

Department of Veterinary Medicine University of Sassari 07100 Sassari Italy

Institute of Microbiology University of Innsbruck A 6020 Innsbruck Austria

Laboratory of Anaerobic Microbiology Institute of Animal Physiology and Genetics Czech Academy of Sciences 14220 Prague Czech Republic

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Skapetas B., Bampidis V. Goat production in the world: Present situation and trends. Livest. Res. Rural Dev. 2016;28:200.

Bi Y., Zeng S., Zhang R., Diao Q., Tu Y. Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition. BMC Microbiol. 2018;18:1–11. doi: 10.1186/s12866-018-1213-9. PubMed DOI PMC

Mao S.Y., Zhang R.Y., Wang D.S., Zhu W.Y. Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing. Anaerobe. 2013;24:12–19. doi: 10.1016/j.anaerobe.2013.08.003. PubMed DOI

Nagata R., Kim Y.H., Ohkubo A., Kushibiki S., Ichijo T., Sato S. Effects of repeated subacute ruminal acidosis challenges on the adaptation of the rumen bacterial community in Holstein bulls. J. Dairy Sci. 2018;101:4424–4436. doi: 10.3168/jds.2017-13859. PubMed DOI

Petri R.M., Schwaiger T., Penner G.B., Beauchemin K.A., Forster R.J., McKinnon J.J., McAllister T.A. Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis. Appl. Environ. Microbiol. 2013;79:3744–3755. doi: 10.1128/AEM.03983-12. PubMed DOI PMC

González L.A., Manteca X., Calsamiglia S., Schwartzkopf-Genswein K.S., Ferret A. Ruminal acidosis in feedlot cattle: Interplay between feed ingredients, rumen function and feeding behavior (a review) Anim. Feed Sci. Technol. 2012;172:66–79. doi: 10.1016/j.anifeedsci.2011.12.009. DOI

Khiaosa-ard R., Zebeli Q. Diet-induced inflammation: From gut to metabolic organs and the consequences for the health and longevity of ruminants. Res. Vet. Sci. 2018;120:17–27. doi: 10.1016/j.rvsc.2018.08.005. PubMed DOI

Zebeli Q., Metzler-Zebeli B.U. Interplay between rumen digestive disorders and diet-induced inflammation in dairy cattle. Res. Vet. Sci. 2012;93:1099–1108. doi: 10.1016/j.rvsc.2012.02.004. PubMed DOI

Sun Y.Z., Mao S.Y., Zhu W.Y. Rumen chemical and bacterial changes during stepwise adaptation to a high-concentrate diet in goats. Animal. 2010;4:210–217. doi: 10.1017/S175173110999111X. PubMed DOI

Liu D.C., Zhou X.L., Zhao P.T., Gao M., Han H., Hu H.L. Effects of Increasing Non-Fiber Carbohydrate to Neutral Detergent Fiber Ratio on Rumen Fermentation and Microbiota in Goats. J. Integr. Agric. 2013;12:319–326. doi: 10.1016/S2095-3119(13)60231-2. DOI

Huo W., Zhu W., Mao S. Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats. World J. Microbiol. Biotechnol. 2014;30:669–680. doi: 10.1007/s11274-013-1489-8. PubMed DOI

Wetzels S.U., Mann E., Metzler-Zebeli B.U., Wagner M., Klevenhusen F., Zebeli Q., Schmitz-Esser S. Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. J. Dairy Sci. 2015;98:5572–5587. doi: 10.3168/jds.2014-9166. PubMed DOI

Liu J.H., Bian G.R., Zhu W.Y., Mao S.Y. High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats. Front. Microbiol. 2015;6:167. doi: 10.3389/fmicb.2015.00167. PubMed DOI PMC

Metzler-Zebeli B.U., Schmitz-Esser S., Klevenhusen F., Podstatzky-Lichtenstein L., Wagner M., Zebeli Q. Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats. Anaerobe. 2013;20:65–73. doi: 10.1016/j.anaerobe.2013.02.005. PubMed DOI

Zhang R., Ye H., Liu J., Mao S. High-grain diets altered rumen fermentation and epithelial bacterial community and resulted in rumen epithelial injuries of goats. Appl. Microbiol. Biotechnol. 2017;101:6981–6992. doi: 10.1007/s00253-017-8427-x. PubMed DOI

Grilli D.J., Fliegerová K., Kopečný J., Lama S.P., Egea V., Sohaefer N., Pereyra C., Ruiz M.S., Sosa M.A., Arenas G.N., et al. Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet. Anaerobe. 2016;42:17–26. doi: 10.1016/j.anaerobe.2016.07.002. PubMed DOI

Liu K., Xu Q., Wang L., Wang J., Guo W., Zhou M. The impact of diet on the composition and relative abundance of rumen microbes in goat. Asian-Australas. J. Anim. Sci. 2017;30:531–537. doi: 10.5713/ajas.16.0353. PubMed DOI PMC

Zhang J., Shi H., Wang Y., Li S., Cao Z., Ji S., He Y., Zhang H. Effect of dietary forage to concentrate ratios on dynamic profile changes and interactions of ruminal microbiota and metabolites in holstein heifers. Front. Microbiol. 2017;8:2206. doi: 10.3389/fmicb.2017.02206. PubMed DOI PMC

Tedersoo L., Sánchez-Ramírez S., Kõljalg U., Bahram M., Döring M., Schigel D., May T., Ryberg M., Abarenkov K. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Divers. 2018;90:135–159. doi: 10.1007/s13225-018-0401-0. DOI

Engelking L.R. Textbook of Veterinary Physiological Chemistry. Academic Press; Amsterdam, The Netherlands: 2015. Overview of carbohydrate metabolism; pp. 120–124.

Ljungdahl L.G. The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use. Ann. N. Y. Acad. Sci. 2008;1125:308–321. doi: 10.1196/annals.1419.030. PubMed DOI

Couger M.B., Youssef N.H., Struchtemeyer C.G., Liggenstoffer A.S., Elshahed M.S. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Biotechnol. Biofuels. 2015;8:1–17. doi: 10.1186/s13068-015-0390-0. PubMed DOI PMC

Solomon K.V., Haitjema C.H., Henske J.K., Gilmore S.P., Borges-Rivera D., Lipzen A., Brewer H.M., Purvine S.O., Wright A.T., Theodorou M.K., et al. Early-branching gut fungi possess large, comprehensive array of biomass-degrading enzymes. Science. 2016;351:1192–1195. doi: 10.1126/science.aad1431. PubMed DOI PMC

Orpin C.G. Anaerobic fungi: Taxonomy, biology and distribution in nature. In: Mountford D.O., Orpin C.G., editors. Anaerobic Fungi: Biology, Ecology and Function. Marcel Dekker; New York, NY, USA: 1994. pp. 1–46.

Silanikove N. The physiological basis of adaptation in goats to harsh environments. Small Rumin. Res. 2000;35:181–193. doi: 10.1016/S0921-4488(99)00096-6. DOI

Li D.B., Hou X.Z. Effect of fungal elimination on bacteria and protozoa populations and degradation of straw dry matter in the rumen of sheep and goats. Asian-Australas. J. Anim. Sci. 2007;20:70–74. doi: 10.5713/ajas.2007.70. DOI

Joshi A., Lanjekar V.B., Dhakephalkar P.K., Callaghan T.M., Griffith G.W., Dagar S.S. Liebetanzomyces polymorphus gen. et sp. nov., a new anaerobic fungus (Neocallimastigomycota) isolated from the rumen of a goat. MycoKeys. 2018;40:89–110. doi: 10.3897/mycokeys.40.28337. PubMed DOI PMC

Hanafy R.A., Lanjekar V.B., Dhakephalkar P.K., Callaghan T.M., Dagar S.S., Griffith G.W., Elshahed M.S., Youssef N.H. Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum. Mycologia. 2020;112:1212–1239. doi: 10.1080/00275514.2019.1696619. PubMed DOI

Hanafy R.A., Elshahed M.S., Liggenstoffer A.S., Griffith G.W., Youssef N.H. Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. Mycologia. 2017;109:231–243. doi: 10.1080/00275514.2017.1317190. PubMed DOI

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. Mycologia. 2018;110:513–525. doi: 10.1080/00275514.2018.1466610. PubMed DOI

Stabel M., Hanafy R.A., Schweitzer T., Greif M., Aliyu H., Flad V., Young D., Lebuhn M., Elshahed M.S., Ochsenreither K., et al. Aestipascuomyces dupliciliberans gen. nov, sp. nov., the first cultured representative of the uncultured SK4 clade from aoudad sheep and alpaca. Microorganisms. 2020;8:1734. doi: 10.3390/microorganisms8111734. PubMed DOI PMC

Ho Y., Barr D.J.S., Abdullah N., Jalaludin S., Kudo H. Piromyces spiralis, a new species of anaerobic fungus from the rumen of goat. Mycotaxon. 1993;48:59–68.

Li G.J., Hyde K.D., Zhao R.L., Hongsanan S., Abdel-Aziz F.A., Abdel-Wahab M.A., Alvarado P., Alves-Silva G., Ammirati J.F., Ariyawansa H.A., et al. Fungal diversity notes 253–366: Taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers. 2016;78:1–237. doi: 10.1007/s13225-016-0366-9. DOI

Hanafy R.A., Johnson B., Elshahed M.S., Youssef N.H. Anaeromyces contortus, sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat. Mycologia. 2018;110:502–512. doi: 10.1080/00275514.2018.1465773. PubMed DOI

Ha J.K., Lee S.S., Gao Z., Kim C.H., Kim S.W., Ko J.Y., Cheng K.J. The effect of saturates fatty acid on cellulose digestion by the rumen anaerobic fungus, Neocallimastix frontalis C5-1. Asian-Australas. J. Anim. Sci. J. Anim. Sci. 2001;14:941–946. doi: 10.5713/ajas.2001.941. DOI

Nagpal R., Puniya A.K., Sehgal J.P., Singh K. In vitro fibrolytic potential of anaerobic rumen fungi from ruminants and non-ruminant herbivores. Mycoscience. 2011;52:31–38. doi: 10.1007/S10267-010-0071-6. DOI

Thareja A., Puniya A.K., Goel G., Nagpal R., Sehgal J.P., Singh P.K., Singh K. In vitro degradation of wheat straw by anaerobic fungi from small ruminants. Arch. Anim. Nutr. 2006;60:412–417. doi: 10.1080/17450390600884443. PubMed DOI

Leis S., Dresch P., Peintner U., Fliegerová K., Sandbichler A.M., Insam H., Podmirseg S.M. Finding a robust strain for biomethanation: Anaerobic fungi (Neocallimastigomycota) from the Alpine ibex (Capra ibex) and their associated methanogens. Anaerobe. 2014;29:34–43. doi: 10.1016/j.anaerobe.2013.12.002. PubMed DOI

Liggenstoffer A.S., Youssef N.H., Couger M.B., Elshahed M.S. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J. 2010;4:1225–1235. doi: 10.1038/ismej.2010.49. PubMed DOI

Vinzelj J., Joshi A., Insam H., Podmirseg S.M. Employing anaerobic fungi in biogas production: Challenges & opportunities. Bioresour. Technol. 2020;300:122687. doi: 10.1016/j.biortech.2019.122687. PubMed DOI

Kok C.M., Sieo C.C., Tan H.Y., Saad W.Z., Liang J.B., Ho Y.W. Anaerobic cellulolytic rumen fungal populations in goats fed with and without Leucaena leucocephala hybrid, as determined by real-time PCR. J. Microbiol. 2013;51:700–703. doi: 10.1007/s12275-013-2540-z. PubMed DOI

Wang G., Luo H., Meng K., Wang Y., Huang H., Shi P., Pan X., Yang P., Diao Q., Zhang H., et al. High genetic diversity and different distributions of glycosyl hydrolase family 10 and 11 xylanases in the goat rumen. PLoS ONE. 2011;6:e16731. doi: 10.1371/journal.pone.0016731. PubMed DOI PMC

FASS . In: Guide for the Care and Use of Agricultural Animals in Research and Teaching. 3rd ed. Swanson J.C., McGlone J.J., editors. Federation of Animal Science Societies Inc.; Champaign, IL, USA: 2010.

National Research Council (U.S.) Nutrient Requirements of Small Ruminants: Sheep, Goats, Cervids, and New World Camelids. National Academies Press; Washington, DC, USA: 2007.

AOAC International . In: Official Methods of AOAC International. 17th ed. Horwitz W., Latimer G.W., editors. AOAC International; Gaithersburg, MA, USA: 2005.

Goering H.K., van Soest P.J. Forage Fiber Analysis (Apparatus Reagents, Procedures and Some Applications) United States Department of Agriculture, Government Printing Office; Washington, DC, USA: 1970. Agriculture Handbook.

Van Soest P.J., Robertson J.B., Lewis B.A. Methods for Dietary Fiber, Neutral Detergent Fiber, and Nonstarch Polysaccharides in Relation to Animal Nutrition. J. Dairy Sci. 1991;74:3583–3597. doi: 10.3168/jds.S0022-0302(91)78551-2. PubMed DOI

Crampton E.W., Maynard L.A. The relation of cellulose and lignin content to the nutritive value of animal feeds. J. Nutr. 1938;15:383–395. doi: 10.1093/jn/15.4.383. DOI

Aguilera J.F. Contributions to the knowledge of the energy nutrition of small ruminants, with particular reference to the goat. Arch. Zootec. 2001;50:565–596.

Yu Z., Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 2004;36:808–812. doi: 10.2144/04365ST04. PubMed DOI

Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Lozupone C.A., Turnbaugh P.J., Fierer N., Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA. 2011;108:4516–4522. doi: 10.1073/pnas.1000080107. PubMed DOI PMC

White T.J., Bruns T.D., Lee S.B., Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., White T.J., editors. PCR Protocols: A Guide to Methods and Applications. Academic Press; London, UK: 1990. pp. 315–322.

Hupfauf S., Etemadi M., Fernández-Delgado Juárez M., Gómez-Brandón M., Insam H., Podmirseg S.M. CoMA—An intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS ONE. 2020;15:e0243241. doi: 10.1371/journal.pone.0243241. PubMed DOI PMC

Pauvert C., Buée M., Laval V., Edel-Hermann V., Fauchery L., Gautier A., Lesur I., Vallance J., Vacher C. Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecol. 2019;41:23–33. doi: 10.1016/j.funeco.2019.03.005. DOI

Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016;13:581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12. doi: 10.14806/ej.17.1.200. DOI

Abarenkov K., Zirk A., Piirmann T., Pöhönen R., Ivanov F., Nilsson R., Henrik R.H., Kõljalg U. UNITE General FASTA Release for Fungi 2. UNITE Community; London, UK: 2020. Version 04.02.2020.

Lee M. Happy Belly Bioinformatics: An open-source resource dedicated to helping biologists utilize bioinformatics. J. Open Source Educ. 2019;2:53. doi: 10.21105/jose.00053. DOI

Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

McMurdie P.J., Holmes S. Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 2013;8:e61217. doi: 10.1371/journal.pone.0061217. PubMed DOI PMC

Gardes M., Bruns T.D. ITS primers with enhanced specificity for Basidiomycetes—Application to the identification of mycorrhizas and rusts. Mol. Ecol. 1993;2:113–118. doi: 10.1111/j.1365-294X.1993.tb00005.x. PubMed DOI

Edwards J.E., Kingston-Smith A.H., Jimenez H.R., Huws S.A., Skøt K.P., Griffith G.W., McEwan N.R., Theodorou M.K. Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen. FEMS Microbiol. Ecol. 2008;66:537–545. doi: 10.1111/j.1574-6941.2008.00563.x. PubMed DOI

Mura E., Edwards J., Kittelmann S., Kaerger K., Voigt K., Mrázek J., Moniello G., Fliegerova K. Anaerobic fungal communities differ along the horse digestive tract. Fungal Biol. 2019;123:240–246. doi: 10.1016/j.funbio.2018.12.004. PubMed DOI

Nagler M., Podmirseg S.M., Griffith G.W., Insam H., Ascher-Jenull J. The use of extracellular DNA as a proxy for specific microbial activity. Appl. Microbiol. Biotechnol. 2018;102:2885–2898. doi: 10.1007/s00253-018-8786-y. PubMed DOI PMC

Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich K., Gordon J.I., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303. PubMed DOI PMC

Koetschan C., Kittelmann S., Lu J., Al-Halbouni D., Jarvis G.N., Müller T., Wolf M., Janssen P.H. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota) PLoS ONE. 2014;9:e91928. doi: 10.1371/journal.pone.0091928. PubMed DOI PMC

Øvreås L., Forney L., Daae F.L., Torsvik V. Distribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 1997;63:3367–3373. doi: 10.1128/AEM.63.9.3367-3373.1997. PubMed DOI PMC

Stahl D.A., Amann R. Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E., Goodfellow M., editors. Nucleic Acid Techniques in Bacterial Systematics. Wiley & Sons Ltd.; Chichester, UK: 1991. pp. 205–248.

Kittelmann S., Naylor G.E., Koolaard J.P., Janssen P.H. A proposed taxonomy of anaerobic fungi (class neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis. PLoS ONE. 2012;7:e36866. doi: 10.1371/journal.pone.0036866. PubMed DOI PMC

Henderson G., Cox F., Ganesh S., Jonker A., Young W., Janssen P.H., Abecia L., Angarita E., Aravena P., Arenas G.N., et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 2015;5:14567. doi: 10.1038/srep14567. PubMed DOI PMC

Gruninger R.J., Ribeiro G.O., Cameron A., McAllister T.A. Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants. Animal. 2019;13:1843–1854. doi: 10.1017/S1751731119000752. PubMed DOI

Guevara J.C., Grünwaldt E.G., Estevez O.R., Bisigato A.J., Blanco L.J., Biurrun F.N., Ferrando C.A., Chirino C.C., Morici E., Fernández B., et al. Range and livestock production in the Monte Desert, Argentina. J. Arid Environ. 2009;73:228–237. doi: 10.1016/j.jaridenv.2008.02.001. DOI

Allegretti L., Sartor C., Paez Lama S., Egea V., Fucili M., Passera C. Effect of the physiological state of Criollo goats on the botanical composition of their diet in NE Mendoza, Argentina. Small Rumin. Res. 2012;103:152–157. doi: 10.1016/j.smallrumres.2011.09.018. DOI

Klevenhusen F., Hollmann M., Podstatzky-Lichtenstein L., Krametter-Frötscher R., Aschenbach J.R., Zebeli Q. Feeding barley grain-rich diets altered electrophysiological properties and permeability of the ruminal wall in a goat model. J. Dairy Sci. 2013;96:2293–2302. doi: 10.3168/jds.2012-6187. PubMed DOI

Khafipour E., Li S., Plaizier J.C., Krause D.O. Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Appl. Environ. Microbiol. 2009;75:7115–7124. doi: 10.1128/AEM.00739-09. PubMed DOI PMC

Lee M., Jeong S., Seo J., Seo S. Changes in the ruminal fermentation and bacterial community structure by a sudden change to a high-concentrate diet in Korean domestic ruminants. Asian-Australas. J. Anim. Sci. 2019;32:92–102. doi: 10.5713/ajas.18.0262. PubMed DOI PMC

Han X., Yang Y., Yan H., Wang X., Qu L., Chen Y. Rumen bacterial diversity of 80 to 110-day-old goats using 16S rRNA sequencing. PLoS ONE. 2015;10:e0117811. doi: 10.1371/journal.pone.0117811. PubMed DOI PMC

Wang L., Xu Q., Kong F., Yang Y., Wu D., Mishra S., Li Y. Exploring the goat rumen microbiome from seven days to two years. PLoS ONE. 2016;11:e0154354. doi: 10.1371/journal.pone.0154354. PubMed DOI PMC

Hua C., Tian J., Tian P., Cong R., Luo Y., Geng Y., Tao S., Ni Y., Zhao R. Feeding a high concentration diet induces unhealthy alterations in the composition and metabolism of ruminal microbiota and host response in a goat model. Front. Microbiol. 2017;8:138. doi: 10.3389/fmicb.2017.00138. PubMed DOI PMC

Cunha I.S., Barreto C.C., Costa O.Y.A., Bomfim M.A., Castro A.P., Kruger R.H., Quirino B.F. Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe. 2011;17:118–124. doi: 10.1016/j.anaerobe.2011.04.018. PubMed DOI

Wang Z., Elekwachi C.O., Jiao J., Wang M., Tang S., Zhou C., Tan Z., Forster R.J. Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats. Sci. Rep. 2017;7:422. doi: 10.1038/s41598-017-00500-5. PubMed DOI PMC

Ebrahimi S.H., Valizade R., Heidarian Miri V. Rumen microbial community of Saanen goats adapted to a high-fiber diet in the Northeast of Iran. Iran. J. Appl. Anim. Sci. 2018;8:271–279.

Kumar S., Indugu N., Vecchiarelli B., Pitta D.W. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows. Front. Microbiol. 2015;6:781. doi: 10.3389/fmicb.2015.00781. PubMed DOI PMC

Jin W., Cheng Y.F., Mao S.Y., Zhu W.Y. Isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane. Bioresour. Technol. 2011;102:7925–7931. doi: 10.1016/j.biortech.2011.06.026. PubMed DOI

Belanche A., Kingston-Smith A.H., Griffith G.W., Newbold C.J. A multi-kingdom study reveals the plasticity of the rumen microbiota in response to a shift from non-grazing to grazing diets in sheep. Front. Microbiol. 2019;10 doi: 10.3389/fmicb.2019.00122. PubMed DOI PMC

Deusch S., Camarinha-Silva A., Conrad J., Beifuss U., Rodehutscord M., Seifert J. A structural and functional elucidation of the rumen microbiome influenced by various diets and microenvironments. Front. Microbiol. 2017;8:1605. doi: 10.3389/fmicb.2017.01605. PubMed DOI PMC

Ishaq S.L., AlZahal O., Walker N., McBride B. An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation. Front. Microbiol. 2017;8:1943. doi: 10.3389/fmicb.2017.01943. PubMed DOI PMC

Alexander H.M. Disease in natural plant populations, communities, and ecosystems: Insights into ecological and evolutionary processes. Plant Dis. 2010;94:492–503. doi: 10.1094/PDIS-94-5-0492. PubMed DOI

Gallo A., Giuberti G., Frisvad J.C., Bertuzzi T., Nielsen K.F. Review on mycotoxin issues in ruminants: Occurrence in forages, effects of mycotoxin ingestion on health status and animal performance and practical strategies to counteract their negative effects. Toxins. 2015;7:3057–3111. doi: 10.3390/toxins7083057. PubMed DOI PMC

Denman S.E., Nicholson M.J., Brookman J.L., Theodorou M.K., McSweeney C.S. Detection and monitoring of anaerobic rumen fungi using an ARISA method. Lett. Appl. Microbiol. 2008;47:492–499. doi: 10.1111/j.1472-765X.2008.02449.x. PubMed DOI

Tapio I., Fischer D., Blasco L., Tapio M., Wallace R.J., Bayat A.R., Ventto L., Kahala M., Negussie E., Shingfield K.J., et al. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS ONE. 2017;12:1–21. doi: 10.1371/journal.pone.0180260. PubMed DOI PMC

Boots B., Lillis L., Clipson N., Petrie K., Kenny D.A., Boland T.M., Doyle E. Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet. J. Appl. Microbiol. 2013;114:626–635. doi: 10.1111/jam.12067. PubMed DOI

Hanafy R.A., Johnson B., Youssef N.H., Elshahed M.S. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ. Microbiol. 2020;22:3883–3908. doi: 10.1111/1462-2920.15164. PubMed DOI

Paul S.S., Bu D., Xu J., Hyde K.D., Yu Z. A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework. Fungal Divers. 2018;89:253–266. doi: 10.1007/s13225-018-0396-6. DOI

Edwards J.E., Forster R.J., Callaghan T.M., Dollhofer V., Dagar S.S., Cheng Y., Chang J., Kittelmann S., Fliegerova K., Puniya A.K., et al. PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: Insights, challenges and opportunities. Front. Microbiol. 2017;8:1657. doi: 10.3389/fmicb.2017.01657. PubMed DOI PMC

Trinci A.P.J., Davies D.R., Gull K., Lawrence M.I., Bonde Nielsen B., Rickers A., Theodorou M.K. Anaerobic fungi in herbivorous animals. Mycol. Res. 1994;98:129–152. doi: 10.1016/S0953-7562(09)80178-0. DOI

Orpin C.G., Joblin K.N. The rumen anaerobic fungi. In: Hobson P.N., Stewart C.S., editors. The Rumen Microbial Ecosystem. Springer; Dordrecht, Germany: 1997. pp. 140–195.

Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W., Bolchacova E., Voigt K., Crous P.W., et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA. 2012;109:6241–6246. doi: 10.1073/pnas.1117018109. PubMed DOI PMC

Blaalid R., Kumar S., Nilsson R.H., Abarenkov K., Kirk P.M., Kauserud H. ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol. Ecol. Resour. 2013;13:218–224. doi: 10.1111/1755-0998.12065. PubMed DOI

Wang X.C., Liu C., Huang L., Bengtsson-Palme J., Chen H., Zhang J.H., Cai D., Li J.Q. ITS1: A DNA barcode better than ITS2 in eukaryotes? Mol. Ecol. Resour. 2015;15:573–586. doi: 10.1111/1755-0998.12325. PubMed DOI

Edwards J.E., Hermes G.D.A., Kittelmann S., Nijsse B., Smidt H. Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis. Front. Microbiol. 2019;10:2317. doi: 10.3389/fmicb.2019.02370. PubMed DOI PMC

Yang R.H., Su J.H., Shang J.J., Wu Y.Y., Li Y., Bao D.P., Yao Y.J. Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing. PLoS ONE. 2018;13:e0206428. doi: 10.1371/journal.pone.0206428. PubMed DOI PMC

Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet