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纤毛虫是纤毛虫门（学名：Ciliophora）生物的通称，是一类较复杂的原生动物，主要特点是以纤毛作为运动器，细胞核一般分化出大核（营养）、小核（生殖）、摄食胞器等，无性生殖为横二分裂，有性生殖为接合生殖，生活在淡水或海水中，也有寄生的[1][2]。代表生物有草履虫，小瓜虫等。
纤毛虫在分类上比较复杂，尚无统一的定论。按传统的分类，原生动物作为动物界中的一个门，纤毛虫为其中的“纤毛纲”（Ciliata），有时也将其列为原生动物门的纤毛亚门，或将原生动物看作动物界的一个亚界，纤毛虫划为一个门——纤毛门。[2]按照汤玛斯·卡弗利尔-史密斯提出的分类系统则属于囊泡藻界的“纤毛虫门”（Ciliophora）。
与其他大部分真核生物不同，纤毛虫有两种大小不同的核：一种是二倍体的小核，负责基因重组；另一种是多倍体的大核，负责一般细胞调控。
食物通过胞吞作用，经过胞口胞咽进入食物泡，通过溶酶体分解使其颗粒变小，能通过膜扩散入细胞质中，残留在食物泡中的物质在胞肛处以胞吐作用排出。 大多数纤毛虫也具有一个或多个突出的收缩泡，收集和排出水以维持细胞内渗透压，以及维持离子平衡。在某些属中（如草履虫），收缩泡有着明显的星状造型，每个星芒都是一个收集管。
纤毛虫都可以进行无性繁殖和有性繁殖。无性繁殖二分裂方式进行，小核发生有丝分裂,大核伸长并分为两半，然后该细胞一分为二。两个新细胞各获得一个大核和一个小核。 与此相反，有性繁殖涉及两个不同交配型（类似性别，但也存在两个以上的交配型）个体之间的结合和遗传物质的交换，这往往发生在食物短缺的时候。
“纤毛虫门”分为两个亚门[3]：
- 核残迹纲 Karyorelictea Corliss，1974
- 异毛纲 Heterotrichea Stein，1859
- 瓶纤纲 Armophorea
- Cariacotrichea
- 叶口纲 Litostomatea Small & Lynn, 1981
属于叶口纲Vestibuliferida目小袋虫科小袋虫属成员的大肠纤毛虫（Balantidium coli）的活动体的图像。 - Subclass Haptoria (e.g. Didinium)
- 毛口亚纲 Trichostomatia Butschli, 1889
- Subclass Rhynchostomatia
- Muranotrichea
- Odontostomatea
- Parablepharismea
- Protocruziea
- 旋毛纲 Spirotrichea Butschli, 1889[4]
- Infraphylum Ventrata[6]
- 肾形虫纲 Colpodea Small & Lynn, 1981[7][8]
- 篮口虫纲 Nassophorea Butschli, 1889
- 寡膜纲 Oligohymenophorea de Puytorac et al., 1974
- 叶咽纲 Phyllopharyngea de Puytorac et al., 1974
- 叶咽亚纲 Phyllopharyngia (e.g. Chilodonella uncinata
- Subclass Rhynchodia
- Subclass Chonotrichia
- 吸管亚纲 Suctoria (e.g. Podophrya)
- Plagiopylea Small & Lynn, 1985
- 前口纲 Prostomatea[11]
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Genus Cryptocaryon（但WoRMS认为属于前口纲前管虫目裸口虫科[12]，只有 Cryptocaryon irritans Brown, 1951一个物种[13]。）
- 纲和目的地位未定的科：
- Cariacotrichidae
- 纲、目和科的地位未定的属：
- Akidodes Lom, 1959
- Allantoxena Yankovskii, 1978
- Allomeron Yankovskii, 1967
- Amoebapium Banina, 1984
- Ampullacula Hsiung, 1930
- Amylophorus Pereira & Almeida, 1942
- Anacharon Ito & Imai, 2000
- Ancistrella Chejsin, 1930
- Andreula Kahl, 1934
- Anglasia Delphy, 1936
- Anisarcon Jankowski, 1981
- Anthochloe Joseph, 1882
- Anthostrombidium Yankovskij, 1980
- Anthurceolaria Jankowski, 1980
- Antipia Lepsi, 1927
- Arcacineta Jankowski, 1981
- Arcodiscophrya Jankowski, 1981
- Armiacineta Yankovskij, 1982
- Asellacineta Jankowski, 1981
- Australana Jankowski, 1986
- Azerella Alekperov, 1985
- Baculiapium Banina, 1984
- Baikalaster Jankowski, 1986
- Baikalonis Yankovskij, 1982
- Baikalotheca Jankowski, 1985
- Baikalothigma Yankovskij, 1982
- Basitokophrya Yankovskij, 1982
- Batiola Koshevoj, 1987
- Baznosanuia Tucolesco, 1962
- Beckmania Yankovskij, 1982
- Beersena Yankovsky, 1989
- Berghophrya Foissner, 2003
- Berounkella Koshevoj, 1987
- Bertolinella Carpano, 1941
- Biconvexellina Konenkova, 1999
- Bignotella Willems, 1975
- Bipalmatum
- Bitricha Cameron, O'Donoghue & Adlard, 2000
- Bizone Lepsi, 1926
- Bizonula Corliss, 1960
- Blepharocodon Bundle, 1895
- Blepharomonas Kopperi, 1937
- Blepharoplanum Kopperi, 1937
- Blepharosphaera Bundle, 1895
- Blepharozoum Gassovsky, 1919
- Borzaiella Makar'eva, 1979
- Bozasella Buisson, 1923
- Buchneriella Heidenreich, 1935
- Buissonella da Cunha & Muniz, 1925
- Buitkampia Foissner, 1985
- Buschiella Corliss, 1960
- Cadosinopsis
- Calix Fraipont, 1878
- Caloscolex Dogiel, 1926
- Calospira Chatton & Lwoff, 1935
- Campanuliapium Banina, 1984
- Campylodinium
- Cardiostomatilla Corliss, 1960
- Carinoposthium Yankovskij, 1980
- Caspionella Yankovskij, 1980
- Caudalina Madhava Rao, 1928
- Causella Aescht, 2001
- Celeritia Tucolesco, 1962
- Cepedella Poyarkoff, 1909
- Cephalospatula Foissner, 2003
- Chanostoma Daday, 1884
- Chattonia Debaisieux, 1957
- Cheissinia Chatton & Lwoff, 1949
- Cheissiniophrya
- Chervurtskella Koshevoj, 1987
- Chilenophrys Jankowski, 1986
- Chlamydonyx Deroux, 1976
- Cinetozona Olmo, Tellez & Esteban, 1998
- Claretinella Keij, 1974
- Claudotricha Gajewskaja, 1925
- Clausophrya Naidenova & Zaika, 1969
- Cochleatina Assejeva, 1983
- Cochliodomus Raabe, 1971
- Colomiellia
- Compactum Hirshfield, Isquith & Bhandary, 1965
- Conchophrys Chatton, 1911
- Conchoscutum Raabe, 1947
- Coniapium Banina, 1984
- Conocladium
- Corlissetta Jankowski, 1986
- Corlissiella Puytorac, 1960
- Coronodiscophrya Jankowski, 1981
- Coronothigma Yankovskij, 1980
- Corynacineta Yankovskii, 1978
- Cotensicoma Yankovskij, 1982
- Cotensita Yankovskij, 1982
- Craspedomyoschiston Jankowski, 1985
- Crassichona Yankovskii, 1973
- Crevicometes Jankowski, 1981
- Cricundella Kofoid & Campbell, 1929
- Crossacineta Yankovskii, 1978
- Cryptacineta Yankovskii, 1978
- Cryptochona Yankovskii, 1973
- Cryptostomina Fedele, 1938
- Ctenochona Yankovskii, 1973
- Cucumophrya Kunz, 1936
- Cunhaia Hasselmann, 1925
- Cunhamunizia Ito & Imai, 2000
- Curviperistomatus Amaro & Sena, 1967
- Cyathopercularia Yankovskij, 1980
- Cylindrapium Banina, 1984
- Cypreostoma Jankowski, 1969
- Cyrtostromhidium
- Daturellina Radoicic, 1959
- Daurotheca Jankowski, 1986
- Delamurea Najdenova, 1978
- Deltacineta Jankowski, 1981
- Dentacinetides Batisse, 1992
- Desicaryon Yankovskii, 1979
- Dicloeopella Eicher, 1965
- Dimaspidisca Yankovskij, 1979
- Dimorphocothurnia Yankovskij, 1980
- Diplogmus Mansfeld, 1923
- Discacineta Jankowski, 1981
- Discephelota Jankowski, 1981
- Discocyathus Jankowski, 1981
- Discomorpha
- Discophryson
- Discophyson Jankowski, 1985
- Discotheca Yankovskii, 1967
- Ditoxum Gassovsky, 1919
- Dolioliapium Banina, 1984
- Drilocineta Raabe, 1972
- Durandella Dragastan, 1972
- Durchoniella Puytorac, 1954
- Echinomeron Yankovskij, 1980
- Echinostrombidium Yankovskij, 1978
- Eilymophrys Corliss, 1979
- Elatodiscophrya Yankovskii, 1978
- Elephantophilus Kofoid, 1935
- Elitarcon Jankowski, 1981
- Elliptothigma
- Elytroplastron Kofoid & MacLennan, 1932
- Eminothigma Corliss, 1979
- Endoralium Eloff & van Hoven, 1980
- Enerthecoma Jarocki, 1935
- Enterophrya Hasselmann, 1918
- Entodiscoides Song, Warren & Wilbert, 1996
- Eodinium Kofoid & MacLennan, 1932
- Epicranella Kofoid & Campbell, 1929
- Epidiophrys Yankovskij, 1979
- Epidiscophrya Jankowski, 1981
- Eriocharon Ito & Imai, 2000
- Estuaricola Yankovskij, 1979
- Eudrilophrya de Puytorac, 1971
- Eurychilum André, 1910
- Extensiscopula Banina, 1984
- Falconyctus Yankovskij, 1978
- Faltacineta Jankowski, 1981
- Ferodiscophrya Jankowski, 1981
- Filiformis Hirshfield, Isquith & Bhandary, 1965
- Fiorentinus Jankowski, 1986
- Fitonacineta Jankowski, 1981
- Foissnerella Jankowski, 1986
- Foliacella Makar'eva, 1979
- Fundenia Vuxanovici, 1962
- Furssenkoiella Makar'eva, 1979
- Gajewskiella Obolkina, 1989
- Gassovskiella Grain, 1994
- Geimania Albaret, 1975
- Georgevitchiella
- Gigantothrix Foissner, 1999
- Grainis Jankowski, 1997
- Gruberella
- Halteroides Hirshfield, Isquith & Bhandary, 1965
- Hastarcon Jankowski, 1981
- Helianter Jankowski, 1969
- Helicozoster
- Heliotheca Yankovskii, 1978
- Hemiprorodon Strelkow, 1939
- Herpetophrya Siedlecki, 1902
- Herpinella Puytorac, 1954
- Holophryoides Gasskovsky, 1919
- Holophryozoon
- Horocontus Deroux, 1976
- Hovasseiella
- Hydrochoerella da Cunha & Muniz, 1925
- Hyloplotes
- Hypophyra López-Ochoterena, 1964
- Hypotrichina
- Hysterophrya de Puytorac, Grolière & Grain, 1979
- Ichthyonyctus Yankovskii, 1974
- Indonyctus Yankovskij, 1978
- Inermichona Jankowski, 1971
- Inferostoma Ki, 1971
- Isopodarcon Jankowski, 1981
- Jankowskia Alekperov, 1984
- Jirovecella Lom, 1957
- Kahlophrya Foissner, 2003
- Kejvia Koshevoj, 1987
- Kellicotta Curds, 1985
- Kindella Yankovskii, 1967
- Kofoidella Cépède, 1910
- Kopperia Corliss, 1960
- Krassnigia
- Kryoprorodon Alekperov & Mamaeva, 1992
- Kudoella Earl, 1972
- Lacifer Yankovskij, 1979
- Ladinosphaera Oberhauser, 1960
- Lagynurus Mansfeld, 1923
- Latteuria Timoshenko & Imai, 1997
- Laurosticha Yankovskij, 1979
- Lavierella Buisson, 1923
- Levanderella Kopperi, 1937
- Limnoricus Jankowski, 1981
- Lissacineta Yankovskii, 1978
- Lissostrombidium Yankovskij, 1978
- Listarcon Yankovskij, 1982
- Litacineta Yankovskii, 1978
- Litosolenius
- Loxocineta Yankovskij, 1979
- Luxiella Lecal, 1953
- Luxophrya Yankovskii, 1978
- Marinecta
- Megadinium
- Membranicola Foissner, Berger & Schaumburg, 1999
- Mesodiscophrya Jankowski, 1981
- Mesogymnus Berger, 1964
- Metaclevelandella
- Metacollinia Yankovskij, 1980
- Metadinium Averintzeff & Mutafova, 1914
- Metaphrya Ikeda, 1917
- Metastomum Georgévitch, 1941
- Microcetella Aescht, 2001
- Micromidas Delphy, 1938
- Micronyctus Yankovskij, 1978
- Micruncus Delphy, 1938
- Mideuplotes Yankovskij, 1978
- Mimeticus Small & Lynn, 1985
- Miniapium Banina, 1984
- Miracineta Jankowski, 1981
- Misacineta Yankovskii, 1978
- Mistarcon
- Mixtophrya de Puytorac, 1969
- Monilidiophrys Yankovskij, 1979
- Monintranstylum
- Monodontophrya Veidovsky, 1892
- Monomastix Roux, 1899
- Monurceolaria Yankovskij, 1980
- Muscophrya Yankovskii, 1978
- Myoscyphidia Jankowski, 1985
- Nematacineta Yankovskii, 1978
- Nemertodendron Yankovskii, 1978
- Netaspidisca Yankovskij, 1978
- Neteuplotes Yankovskij, 1978
- Nipponarcon Jankowski, 1981
- Noracineta Yankovskii, 1978
- Nuchterleinella Matthes, 1990
- Nucleocorbula Santhakumari & Balakrishnan Nair, 1970
- Nucleocorbula adherens [14]
- Ogimotoa Ito & Imai, 2000
- Ogimotopsis Ito & Imai, 2000
- Oldesleria Foissner, 1983
- Olgella Koshevoj, 1987
- Oligoisotricha Imai, 1981
- Ollella Aescht, 2001
- Oncosonderia Yankovskij, 1980
- Ophiodiscus Yankovskii, 1976
- Ophiuraespira
- Ophiurephelota Jankowski, 1981
- Ophryocephalus Wailes, 1925
- Oraveczisphaera Kozur, 1986
- Oreoctoma Yankovskij, 1980
- Orsomia Baer, 1952
- Orthurceolaria Yankovskij, 1980
- Parablaste
- Parabundleia Imai & Ogimoto, 1983
- Paraclevelandia Kidder, 1937
- Paracollinia Yankovskij, 1980
- Paractedectoma
- Paracunhamunizia Ito & Imai, 2000
- Paracycloposthium Grain, 1994
- Paradectoma Small & Lynn, 1985
- Paradentacineta Yankovskii, 1978
- Paradiscophrya Jankowski, 1981
- Parafavelloides
- Paraglaucoma Kahl, 1926
- Paraheliophrya Yankovskii, 1978
- Paraisotrichopsis Gasskovsky, 1919
- Paraloricophrya Yankovskii, 1978
- Paranoplophrya
- Paranyctotherus Ngassam, 1983
- Paraoxychona Yankovskii, 1973
- Paraplagiopyla Thurston & Grain, 1971
- Parapyxicola Jankowski, 1985
- Parasphaerophrya Jankowski, 1981
- Parastylonchia Dragesco, 1963
- Parastylophrya Yankovskii, 1978
- Paratrochilia Kahl, 1933
- Paravauchomia Raabe, 1963
- Parducia
- Parendosphaera Jankowski, 1981
- Parentodinium Thurston & Noirot-Timothee, 1973
- Parhypocoma Chatton & Lwoff, 1939
- Patschia Small & Lynn, 1985
- Peltacineta Yankovskii, 1978
- Perezella Cépède, 1910
- Peristrombidium Yankovskij, 1978
- Perseia Rossolimo, 1926
- Phagoon Foissner, Agatha & Berger, 2002
- Phyllacineta Yankovskii, 1978
- Piesika Warren, 1988
- Pinchatia Shibuya, 1931
- Pingius Hsiung, 1932
- Planitrichidium Yankovskij, 1979
- Pleurophryodendron Yankovskii, 1978
- Podopyrya
- Poljanskina Raabe, 1963
- Polydiniella Corliss, 1960
- Polydiophrys Yankovskij, 1979
- Pompholyxia Fabre-Domergue, 1886
- Poteriapium Banina, 1984
- Pottsia Chatton & Lwoff, 1927
- Pottsiodes Corliss, 1960
- Proamphorella Kofoid & Campbell, 1939
- Proclausilocola Lom, 1959
- Proluxophrya Yankovskii, 1978
- Prorodonopsis Gasskovsky, 1919
- Prostelidiella Kofoid & Campbell, 1939
- Protanoplophrya
- Protocaviella Kopperi, 1937
- Protohallia Cunha & Muniz, 1927
- Protoisotricha Kopperi, 1937
- Protolutzia Cunha & Muniz, 1925
- Protophryopsis
- Protoradiophryopsis Georgévitch, 1949
- Protospirella Aescht, 2001
- Prototravassosia
- Pseudarcella
- Pseudobalanion Foissner, Oleksiv & Müller, 1990
- Pseudocinetochilum Timoshkin, 1995
- Pseudocristigera Horvath, 1956
- Pseudoentodinium Wolska, 1986
- Pseudonyctotherus Earl, 1970
- Pterochona Jankowski, 1973
- Pterodiniella Aescht, 2001
- Radiophryopsis Georgévitch, 1941
- Rattulus
- Rectiperistomatus Amaro & Sena, 1968
- Recurviperistomatus Amaro & Sena, 1967
- Rhabdothoracella Aescht, 2001
- Rhinodisculus Mansfeld, 1923
- Rhizobranchium Jankowski, 1981
- Rhizocaryum Caullery & Mesnil, 1907
- Rhizotricha Wolska, 1964
- Rhynchodinium Cunha & Penido, 1927
- Riboscyphidia Yankovskij, 1980
- Riftus Jankowski, 1981
- Riftus Yankovskij, 1982
- Rimacineta Jankowski, 1981
- Rondacineta Yankovskii, 1978
- Rondosomides Jankowski, 1981
- Roquea Jankowski, 1967
- Rossielella Aescht, 2001
- Rossonophrys Jankowski, 1989
- Rugaecaulis Lom & de Puytorac, 1994
- Sannemannisphaera Kozur, 1986
- Saragassephelota
- Sargassephelota Jankowski, 1981
- Savroniella Bielokrys, 1995
- Scalpratella Makar'eva, 1979
- Schedotrochilia Deroux, 1976
- Schizactinia
- Sciurula Corliss, 1960
- Scopulata Viljoen & van As, 1985
- Scythiana Haas, Tóthne Makk, Oraveczne Scheffer & Csalagovits, 1986
- Semiacineta Yankovskii, 1978
- Seravinella Alekperov & Mamaeva, 1992
- Sertumia Tucolesco, 1962
- Setarcon Jankowski, 1981
- Setodiscophrya Jankowski, 1981
- Severonis Jankowski, 1981
- Shellephelota Jankowski, 1981
- Sibiracineta Yankovskij, 1982
- Sigmaperistomatus Amaro & Sena, 1968
- Sigmocineta Jankowski, 1967
- Sigmophrya de Puytorac, 1971
- Silenella Fenchel, 1965
- Sincothurnia Jankowski, 1985
- Soracineta Yankovskii, 1978
- Sparsacineta Yankovskii, 1978
- Speleoscyphidia Yankovskij, 1980
- Spherasuctans Puytorac, 1952
- Spinarcella
- Spinarcon Jankowski, 1981
- Spinivorticella Jankowski, 1993
- Spinophenia Szczechura, 1969
- Spirocystomellites
- Spirogonella Yankovskij, 1978
- Spiroperistomatus Amaro & Sena, 1968
- Spiroxystonella Kofoid & Campbell, 1939
- Spiroxystonellites Knauer, 1969
- Spongiarcon Yankovskij, 1980
- Spongiocirrhus Yankovskij, 1979
- Spongiophrya Yankovskii, 1978
- Stemacineta Yankovskii, 1978
- Stenophaga Jankowski, 1981
- Stentofollicullina
- Stentoropsis Dogiel & Bychowsky, 1934
- Stylarcon Jankowski, 1981
- Stylogemma Jankowski, 1981
- Stylophryodendron Yankovskii, 1978
- Sulcoarcus Hsiung, 1935
- Sulfonecta Yankovskij, 1978
- Syllarcon Jankowski, 1981
- Syncilancistrumina Knight & Thorne, 1982
- Synophrya Chatton & Lwoff, 1926
- Taeniocineta Raabe, 1972
- Talitrochilodon Yankovskij, 1980
- Talizona Jankowski, 1981
- Tauriella Naidenova, 1985
- Telamodinium
- Teratodinium
- Teremanticola Yankovskij, 1980
- Teretrichodina Yankovskij, 1980
- Ternacineta Yankovskii, 1978
- Tesnotheca Jankowski, 1986
- Testudinicola Yankovskii, 1978
- Tetratoxum Gasskovsky, 1919
- Thalassacineta Jankowski, 1981
- Thalassicineta
- Thalassiomastix Busch, 1923
- Thalassochona Yankovskii, 1971
- Thaumatophrya Collin, 1912
- Thigmostrombidium Yankovskij, 1978
- Thigmozoon Santhakumari & Balakrishnan Nair, 1973
- Thisarcon
- Thoracodinium Latteur, 1960
- Tokophryona Yankovskij, 1982
- Tomodiscophrya Jankowski, 1981
- Toxodinium da Cunha, 1938
- Toxopercularia Yankovskii, 1980
- Triacola Weitschat & Guhl, 1994
- Tricaudalia Buisson, 1923
- Trinacineta Jankowski, 1981
- Tripalmaria Gasskovsky, 1919
- Tucolesca Lom, 1979
- Tundrella Koshevoj, 1987
- Tytthocorys Tappan & Loeblich, 1968
- Uropogon Ito & Imai, 2000
- Uvelinus Jankowski, 1985
- Vasacineta Jankowski, 1981
- Vautrinella Cuvillier, 1957
- Velavella Koshevoj, 1987
- Velistoma Yankovskij, 1980
- Venodiscophrya Jankowski, 1981
- Veracineta Yankovskii, 1978
- Vesonyctus
- Vestonyctus Yankovskij, 1978
- Vinarcon Jankowski, 1981
- Vostonica Jankowski, 1994
- Wailesia Kofoid & Campbell, 1939
- Wichtermania Earl, 1972
- Yvonniellina Tappan & Loeblich, 1968
- Zonotrichium Meunier, 1910
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