{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:42:54Z","timestamp":1760150574297,"version":"build-2065373602"},"reference-count":56,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T00:00:00Z","timestamp":1702598400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Grant Scientific Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and the Slovak Academy of Sciences","award":["VEGA 2\/0009\/08","VEGA 2\/0008\/21"],"award-info":[{"award-number":["VEGA 2\/0009\/08","VEGA 2\/0008\/21"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E.\u00a0parvicaudatum prevailed (70%). The DNA of four individual E.\u00a0parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350\u2013400 bp) were identical to Epidinium sequences in GenBank (E.\u00a0caudatum, a one-spine morphotype, and E.\u00a0cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.<\/jats:p>","DOI":"10.3390\/life13122350","type":"journal-article","created":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T08:12:57Z","timestamp":1702627977000},"page":"2350","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus"],"prefix":"10.3390","volume":"13","author":[{"given":"Silvia","family":"Ivorov\u00e1","sequence":"first","affiliation":[{"name":"Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Ko\u0161ice, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3054-7010","authenticated-orcid":false,"given":"Anna","family":"Kop\u010dakov\u00e1","sequence":"additional","affiliation":[{"name":"Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Ko\u0161ice, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Prista\u0161","sequence":"additional","affiliation":[{"name":"Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Ko\u0161ice, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6608-4903","authenticated-orcid":false,"given":"Svetlana","family":"Ki\u0161idayov\u00e1","sequence":"additional","affiliation":[{"name":"Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Ko\u0161ice, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1111\/jeu.12391","article-title":"Beyond the \u201cCode\u201d: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)","volume":"64","author":"Warren","year":"2017","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1016\/j.ympev.2015.10.017","article-title":"Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists","volume":"94","author":"Zhao","year":"2016","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Jia, T.Z., Caudan, M., and Mamajanov, I. (2021). Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution. Life, 11.","DOI":"10.3390\/life11020154"},{"key":"ref_4","unstructured":"Mallet, J. (2013). Encyclopedia of Biodiversity, Elsevier."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1086\/419370","article-title":"Biodiversity at the Microbial Level: The Number of Free-Living Ciliates in the Biosphere","volume":"71","author":"Finlay","year":"1996","journal-title":"Q. Rev. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1111\/jeu.12211","article-title":"Molecular Phylogeny of the Family Ophryscolecidae (Ciliophora, Litostomatea) Inferred from 18S rDNA Sequences","volume":"62","author":"Rossi","year":"2015","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"8","DOI":"10.2108\/zs140125","article-title":"Methods for Taxonomic Studies of Rumen Ciliates (Alveolata: Ciliophora): A Brief Review","volume":"32","author":"Cedrola","year":"2015","journal-title":"Zool. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1128\/AEM.03697-14","article-title":"Phylogeny of Intestinal Ciliates, Including Charonina ventriculi, and Comparison of Microscopy and 18S rRNA Gene Pyrosequencing for Rumen Ciliate Community Structure Analysis","volume":"81","author":"Kittelmann","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.ejop.2017.01.004","article-title":"Investigating the biodiversity of ciliates in the \u2018Age of Integration\u2019","volume":"61","author":"Clamp","year":"2017","journal-title":"Eur. J. Protistol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"West-Eberhard, M.J. (2008). Phenotypic Plasticity. Encycl. Ecol., 2701\u20132707.","DOI":"10.1016\/B978-008045405-4.00837-5"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Williams, A.G., and Coleman, G.S. (1992). The Rumen Protozoa, Springer.","DOI":"10.1007\/978-1-4612-2776-2"},{"key":"ref_12","unstructured":"Ogimoto, K., and Imai, S. (1981). Atlas of Rumen Microbiology, Japan Scientific Societies Press."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Cedrola, F., Senra, M.V.X., Fregulia, P., D\u2019agosto, M., and Dias, R.J.P. (2022). Insights into the systematics of the family Ophryoscolecidae (Ciliophora, Entodiniomorphida). J. Eukaryot. Microbiol., 69.","DOI":"10.1111\/jeu.12915"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"249","DOI":"10.11646\/zootaxa.4306.2.5","article-title":"Polymorphism and inconsistencies in the taxonomy of Diplodinium anisacanthum da Cunha, 1914 (Ciliophora, Entodiniomorphida, Ophryoscolecidae) and taxonomic notes on the genus Diplodinium Schuberg, 1888","volume":"4306","author":"Cedrola","year":"2017","journal-title":"Zootaxa"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1111\/j.1550-7408.1994.tb01481.x","article-title":"Rumen Ciliate Protozoa of the Blue Duiker (Cephalophus monticola), with Observations on Morphological Variation Lines Within the Species Entodinium dubardi","volume":"41","author":"Dehority","year":"1994","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_16","first-page":"164","article-title":"Observation on the growth and morphological variability of the rumen ciliates Epidinium caudatum f. fasciculus cultured in vitro","volume":"17","author":"Miltko","year":"2006","journal-title":"Endocytobiosis Cell Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"35","DOI":"10.22358\/jafs\/70137\/2006","article-title":"Factors influencing morphological variability of rumen ciliates from the genus Ophryoscolex","volume":"15","author":"Miltko","year":"2006","journal-title":"J. Anim. Feed Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"33","DOI":"10.11646\/zootaxa.1305.1.3","article-title":"Studies on the variation in caudal spination of Epidinium","volume":"1305","author":"Dehority","year":"2006","journal-title":"Zootaxa"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1099\/00221287-73-3-509","article-title":"The Cultivation of the Rumen Ciliates Epidinium ecaudatum caudatum and Polyplastron multivesiculatum in vitro","volume":"73","author":"Coleman","year":"1972","journal-title":"J. Gen. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1099\/00221287-101-2-253","article-title":"The Cultivation of the Rumen Ciliate Entodinium bursa in the Presence of Entodinium caudatum","volume":"101","author":"Coleman","year":"1977","journal-title":"J. Gen. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1099\/00221287-33-3-401","article-title":"The Cultivation of Some Rumen Oligotrich Protozoa","volume":"33","author":"Clarke","year":"1963","journal-title":"J. Gen. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1111\/j.1550-7408.1964.tb01796.x","article-title":"Factors Influencing the in vitro Culture of the Rumen Ciliate Ophryoscolex purkynei Stein","volume":"11","author":"Mah","year":"1964","journal-title":"J. Protozool."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1292\/jvms1939.43.359","article-title":"Ciliate protozoa from the rumen of the Japanese serow, Capricornis crispus (Temminck)","volume":"43","author":"Imai","year":"1981","journal-title":"Jpn. J. Vet. Sci."},{"key":"ref_24","unstructured":"Fiorentini, A. (1889). Intorno ai Protisti Stomaco dei Bovini, Frat Fusi."},{"key":"ref_25","first-page":"1","article-title":"Monographie der Familie Ophryoscolecidae","volume":"59","author":"Dogiel","year":"1927","journal-title":"Teil I. Arch fur Protistenkd."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Sharp, R.C. (1914). Diplodinium ecaudatum with an Account of Its Neuromotor Apparatus, University of California Press.","DOI":"10.5962\/bhl.title.28194"},{"key":"ref_27","first-page":"87","article-title":"Studies on parasitic ciliates from Indian ruminants","volume":"8","author":"Banerjee","year":"1955","journal-title":"Proc. Zool. Soc. Bengal."},{"key":"ref_28","first-page":"15","article-title":"Some Rumen Ciliates (Isotrichidae, Trichostomatida; Epidininae, Ophryoscolecidae) of the Domestic Goat (Capra hircus L.) in Turkey","volume":"26","year":"2002","journal-title":"Turkish J. Zool."},{"key":"ref_29","unstructured":"Kofoid, C.A., and MacLennan, R.F. (1933). Ciliates from Bos indicus Linn. III. Epidinium Crawley, Epiplastron Gen. Nov. and Ophryoscolex Stein, University of California Press."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.ejop.2014.01.004","article-title":"The symbiotic intestinal ciliates and the evolution of their hosts","volume":"50","author":"Michalowski","year":"2014","journal-title":"Eur. J. Protistol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ki\u0161idayov\u00e1, S., Durkaj, D., Mihalikov\u00e1, K., V\u00e1radyov\u00e1, Z., Puchalska, J., Szumacher-Strabel, M., Cie\u015blak, A., and Gizejewski, Z. (2021). Rumen Ciliated Protozoa of the Free-Living European Bison (Bison bonasus, Linnaeus). Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.658448"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1111\/j.1550-7408.1997.tb05693.x","article-title":"Phylogeny of the Rumen Ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) Inferred from Small Subunit Ribosomal RNA Sequences","volume":"44","author":"Wright","year":"1997","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_33","first-page":"178","article-title":"Past: Paleontological Statistics Software Package for Education and Data Analysis","volume":"4","author":"Hammer","year":"2001","journal-title":"Palaeontol. Electron."},{"key":"ref_34","unstructured":"Burk, A.D. (1993). Laboratory Manual for Classification and Morphology of Rumen Ciliate Protozoa, CRC Press."},{"key":"ref_35","first-page":"219","article-title":"Rapid identification of rumen protozoa by restriction analysis of amplified 18S rRNA gene","volume":"43","author":"Regensbogenova","year":"2004","journal-title":"Acta Protozool."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.ejop.2010.05.002","article-title":"Physiological characteristics of several rumen protozoa grown in vitro with observations on within and among species variation","volume":"46","author":"Dehority","year":"2010","journal-title":"Eur. J. Protistol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1099\/00221287-29-4-579","article-title":"Inter-Relationships between Certain Rumen Ciliate Protozoa","volume":"29","author":"Eadie","year":"1962","journal-title":"J. Gen. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1590\/S0101-81752008000300010","article-title":"Preda\u00e7\u00e3o e canibalismo entre protozo\u00e1rios ciliados (Ciliophora: Entodiniomorphida: Ophryoscolecidae) no r\u00famen de ovinos (Ovis aries)","volume":"25","author":"Martinele","year":"2008","journal-title":"Rev. Bras. Zool."},{"key":"ref_40","first-page":"69","article-title":"Microbial Interactions in the Rumen","volume":"15","author":"Dehority","year":"1998","journal-title":"Rev. Fac. Agron. (LUZ)"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ab.2013.04.006","article-title":"Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues","volume":"439","author":"Paireder","year":"2013","journal-title":"Anal. Biochem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"104771","DOI":"10.1016\/j.yexmp.2022.104771","article-title":"Fragmentation assessment of FFPE DNA helps in evaluating NGS library complexity and interpretation of NGS results","volume":"126","author":"Ottestad","year":"2022","journal-title":"Exp. Mol. Pathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1007\/s00428-017-2213-0","article-title":"DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks","volume":"471","author":"Guyard","year":"2017","journal-title":"Virchows Arch."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"36","DOI":"10.4132\/KoreanJPathol.2014.48.1.36","article-title":"Effects of Fixation and Storage of Human Tissue Samples on Nucleic Acid Preservation","volume":"48","author":"Nam","year":"2014","journal-title":"Korean J. Pathol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/gim.2017.241","article-title":"Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: Pilot study for the 100,000 Genomes Project","volume":"20","author":"Robbe","year":"2018","journal-title":"Genet Med."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.ab.2009.08.016","article-title":"High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil","volume":"395","author":"Lin","year":"2009","journal-title":"Anal. Biochem."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Wang, Y., Tian, R.M., Gao, Z.M., Bougouffa, S., and Qian, P.-Y. (2014). Optimal Eukaryotic 18S and Universal 16S\/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0090053"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"5515","DOI":"10.1128\/AEM.01644-14","article-title":"Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa","volume":"80","author":"Ishaq","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"812","DOI":"10.2527\/2003.813812x","article-title":"Technical note: Specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows1","volume":"81","author":"Karnati","year":"2003","journal-title":"J. Anim. Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1111\/j.1550-7408.1999.tb04627.x","article-title":"Analysis of intraspecific sequence variation among eight isolates of the rumen symbiont, Isotricha prostoma (Ciliophora), from two continents","volume":"46","author":"Wright","year":"1999","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.ympev.2012.06.024","article-title":"Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)","volume":"65","author":"Bourland","year":"2012","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s13127-020-00469-6","article-title":"Multi-gene phylogeny of the subclass Astomatia (Protista: Ciliophora) refreshed with two rare astome ciliates from the digestive tube of endogeic earthworms","volume":"21","author":"Obert","year":"2021","journal-title":"Org. Divers. Evol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Newbold, C.J., De La Fuente, G., Belanche, A., Ramos-Morales, E., and McEwan, N.R. (2015). The Role of Ciliate Protozoa in the Rumen. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.01313"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.protis.2011.12.002","article-title":"Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea)","volume":"164","author":"Santoferrara","year":"2013","journal-title":"Protist"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1111\/jeu.12414","article-title":"UniEuk: Time to Speak a Common Language in Protistology!","volume":"64","author":"Berney","year":"2017","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Belanche, A., Kingston-Smith, A.H., Griffith, G.W., and Newbold, C.J. (2019). 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., 10.","DOI":"10.3389\/fmicb.2019.00122"}],"container-title":["Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-1729\/13\/12\/2350\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:39:33Z","timestamp":1760132373000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-1729\/13\/12\/2350"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,15]]},"references-count":56,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["life13122350"],"URL":"https:\/\/doi.org\/10.3390\/life13122350","relation":{},"ISSN":["2075-1729"],"issn-type":[{"type":"electronic","value":"2075-1729"}],"subject":[],"published":{"date-parts":[[2023,12,15]]}}}