메뉴 건너뛰기




Volumn 80, Issue 17, 2014, Pages 5515-5521

Design and validation of four new primers for next-generation sequencing to target the 18S rRNA genes of gastrointestinal ciliate protozoa

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALS; RNA;

EID: 84905898382     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01644-14     Document Type: Article
Times cited : (29)

References (46)
  • 1
    • 10644273232 scopus 로고
    • Contribution of rumen protozoa to fibre degradation and cellulase activity in vitro
    • Gijzen HJ, Lubberding HJ, Gerhardus MJT, Vogels GD. 1988. Contribution of rumen protozoa to fibre degradation and cellulase activity in vitro. FEMS Microbiol. Lett. 53:35-43. http://dx.doi.org/10.1111/j.1574 -6968.1988.tb02645.x.
    • (1988) FEMS Microbiol. Lett , vol.53 , pp. 35-43
    • Gijzen, H.J.1    Lubberding, H.J.2    Gerhardus, M.J.T.3    Vogels, G.D.4
  • 2
    • 0024575680 scopus 로고
    • Ruminal cellulolytic bacteria and protozoa from bison, cattle-bison hybrids, and cattle fed three alfalfa-corn diets
    • Varel VH, Dehority BA. 1989. Ruminal cellulolytic bacteria and protozoa from bison, cattle-bison hybrids, and cattle fed three alfalfa-corn diets. Appl. Environ. Microbiol. 55:148-153.
    • (1989) Appl. Environ. Microbiol. , vol.55 , pp. 148-153
    • Varel, V.H.1    Dehority, B.A.2
  • 3
    • 0027338468 scopus 로고
    • Changes in the rumen microbial population and its activities during the refaunation period after the reintroduction of ciliate protozoa into the rumen of defaunated sheep
    • Williams AG, Withers SE. 1993. Changes in the rumen microbial population and its activities during the refaunation period after the reintroduction of ciliate protozoa into the rumen of defaunated sheep. Can. J. Microbiol. 39:61-69. http://dx.doi.org/10.1139/m93-009.
    • (1993) Can. J. Microbiol , vol.39 , pp. 61-69
    • Williams, A.G.1    Withers, S.E.2
  • 4
    • 0001447985 scopus 로고
    • Ophryoscolecidae from the stomach of Cervus elaphus L., Dama dama L., and Capreolus capreolus L
    • (In Czech.)
    • Sládeček F. 1946. Ophryoscolecidae from the stomach of Cervus elaphus L., Dama dama L., and Capreolus capreolus L. Vestn. Cesk. Zool. Spol. 10:201-231. (In Czech.)
    • (1946) Vestn. Cesk. Zool. Spol. , vol.10 , pp. 201-231
    • Sládecek, F.1
  • 5
    • 84989993549 scopus 로고
    • Observations on the morphology and division of Eudiplodinium neglectum Dogiel (Ciliata Entodiniomorpha) from the stomach of a moose (Alces americana)
    • Krascheninnikow S. 1955. Observations on the morphology and division of Eudiplodinium neglectum Dogiel (Ciliata Entodiniomorpha) from the stomach of a moose (Alces americana). J. Protozool. 2:124-134. http://dx.doi.org/10.1111/j.1550-7408.1955.tb02412.x.
    • (1955) J. Protozool , vol.2 , pp. 124-134
    • Krascheninnikow, S.1
  • 6
    • 0016031240 scopus 로고
    • Rumen ciliate fauna of Alaskan moose (Alces americana), musk-ox (Ovibos moschatus) and Dall mountain sheep (Ovis dalli)
    • Dehority BA. 1974. Rumen ciliate fauna of Alaskan moose (Alces americana), musk-ox (Ovibos moschatus) and Dall mountain sheep (Ovis dalli). J. Eukaryot. Microbiol. 21:26-32.
    • (1974) J. Eukaryot. Microbiol. , vol.21 , pp. 26-32
    • Dehority, B.A.1
  • 7
    • 0017185762 scopus 로고
    • The cultivation of cellulolytic protozoa isolated from the rumen
    • Coleman GS, Laurie JI, Bailey JE, Holdgate SA. 1976. The cultivation of cellulolytic protozoa isolated from the rumen. J. Gen. Microbiol. 95:144- 150. http://dx.doi.org/10.1099/00221287-95-1-144.
    • (1976) J. Gen. Microbiol , vol.95 , pp. 144-150
    • Coleman, G.S.1    Laurie, J.I.2    Bailey, J.E.3    Holdgate, S.A.4
  • 8
    • 0020771440 scopus 로고
    • Association of methanogenic bacteria with rumen protozoa
    • Krumholz LR, Forsberg CW, Veira DM. 1983. Association of methanogenic bacteria with rumen protozoa. Can. J. Microbiol. 29:676-680. http://dx.doi.org/10.1139/m83-110.
    • (1983) Can. J. Microbiol , vol.29 , pp. 676-680
    • Krumholz, L.R.1    Forsberg, C.W.2    Veira, D.M.3
  • 9
    • 2342481668 scopus 로고    scopus 로고
    • Rumen ciliate protozoal fauna of reindeer in Inner Mongolia
    • Imai S, Oku Y, Morita T, Ike K, Guirong. 2004. Rumen ciliate protozoal fauna of reindeer in Inner Mongolia, China. J. Vet. Med. Sci. 66:209-212. http://dx.doi.org/10.1292/jvms.66.209.
    • (2004) China. J. Vet. Med. Sci , vol.66 , pp. 209-212
    • Imai, S.1    Oku, Y.2    Morita, T.3    Ike, K.4    Guirong5
  • 10
    • 0031278876 scopus 로고    scopus 로고
    • Ciliate protozoa in the rumen of Sassaby antelope, Damaliscus lunatus lunatus, including the description of a new species and form
    • Ito A, Arai N, Tsutsumi Y, Imai S. 2007. Ciliate protozoa in the rumen of Sassaby antelope, Damaliscus lunatus lunatus, including the description of a new species and form. J. Eukaryot. Microbiol. 44:586-591. http://dx.doi.org/10.1111/j.1550-7408.1997.tb05964.x.
    • (2007) J. Eukaryot. Microbiol , vol.44 , pp. 586-591
    • Ito, A.1    Arai, N.2    Tsutsumi, Y.3    Imai, S.4
  • 11
    • 0038608039 scopus 로고    scopus 로고
    • Specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows
    • Karnati SKR, Yu Z, Sylvester JT, Dehority BA, Morrison M, Firkins JL. 2003. Specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows. J. Anim. Sci. 81:812-815.
    • (2003) J. Anim. Sci. , vol.81 , pp. 812-815
    • Karnati, S.K.R.1    Yu, Z.2    Sylvester, J.T.3    Dehority, B.A.4    Morrison, M.5    Firkins, J.L.6
  • 12
    • 10044284420 scopus 로고    scopus 로고
    • Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR
    • Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL. 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J. Nutr. 134:3378-3384.
    • (2004) J. Nutr. , vol.134 , pp. 3378-3384
    • Sylvester, J.T.1    Karnati, S.K.R.2    Yu, Z.3    Morrison, M.4    Firkins, J.L.5
  • 13
    • 78751683250 scopus 로고    scopus 로고
    • Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries
    • Kittelmann S, Janssen PH. 2011. Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries. FEMS Microbiol. Ecol. 75:468-481. http://dx.doi.org/10.1111/j.1574-6941.2010.01022.x.
    • (2011) FEMS Microbiol. Ecol , vol.75 , pp. 468-481
    • Kittelmann, S.1    Janssen, P.H.2
  • 15
    • 0035252376 scopus 로고    scopus 로고
    • Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity
    • Moon-van der Staay SY, De Wachter R, Vaulot D. 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607-610. http://dx.doi.org/10.1038/35054541.
    • (2001) Nature , vol.409 , pp. 607-610
    • Moon-van der Staay, S.Y.1    De Wachter, R.2    Vaulot, D.3
  • 16
    • 35948999735 scopus 로고    scopus 로고
    • Cultivationindependent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil
    • Lara E, Berney C, Harms H, Chatzinotas A. 2007. Cultivationindependent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. FEMS Microbiol. Ecol. 62:365-373. http://dx.doi.org/10.1111/j.1574-6941.2007.00387.x.
    • (2007) FEMS Microbiol. Ecol , vol.62 , pp. 365-373
    • Lara, E.1    Berney, C.2    Harms, H.3    Chatzinotas, A.4
  • 17
    • 40849114656 scopus 로고    scopus 로고
    • Molecular characterization of ciliate diversity in stream biofilms
    • Dopheide A, Lear G, Stott R, Lewis G. 2008. Molecular characterization of ciliate diversity in stream biofilms. Appl. Environ. Microbiol. 74:1740- 1747. http://dx.doi.org/10.1128/AEM.01438-07.
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 1740-1747
    • Dopheide, A.1    Lear, G.2    Stott, R.3    Lewis, G.4
  • 18
    • 68149178616 scopus 로고    scopus 로고
    • A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes
    • Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One 4:e6372. http://dx.doi.org/10.1371/journal.pone.0006372.
    • (2009) PLoS One , vol.4
    • Amaral-Zettler, L.A.1    McCliment, E.A.2    Ducklow, H.W.3    Huse, S.M.4
  • 20
    • 84873684861 scopus 로고    scopus 로고
    • Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities
    • Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R. 2013. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One 8:e47879. http://dx.doi.org/10.1371/journal.pone.0047879.
    • (2013) PLoS One , vol.8
    • Kittelmann, S.1    Seedorf, H.2    Walters, W.A.3    Clemente, J.C.4    Knight, R.5
  • 21
    • 79953180038 scopus 로고    scopus 로고
    • Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction
    • Xie Q, Lin J, Qin Y, Zhou J, Bu W. 2011. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction. Protein Cell 2:161-170. http://dx.doi.org/10.1007/s13238 -011-1017-2.
    • (2011) Protein Cell , vol.2 , pp. 161-170
    • Xie, Q.1    Lin, J.2    Qin, Y.3    Zhou, J.4    Bu, W.5
  • 22
    • 0030893569 scopus 로고    scopus 로고
    • Phylogeny of the rumen ciliates Entodinium Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences
    • Wright A-DG, Dehority BA, Lynn DH. 1997. Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J. Eukaryot. 44:61- 67. http://dx.doi.org/10.1111/j.1550-7408.1997.tb05693.x.
    • (1997) J. Eukaryot. , vol.44 , pp. 61-67
    • Wright, A.-D.G.1    Dehority, B.A.2    Lynn, D.H.3
  • 23
    • 0031407579 scopus 로고    scopus 로고
    • Maximum ages of ciliate lineages estimated using a small subunit rRNA molecular clock: crown eukaryotes that date back to the Paleoproterozoic
    • Wright A-DG, Lynn DH. 1997. Maximum ages of ciliate lineages estimated using a small subunit rRNA molecular clock: crown eukaryotes that date back to the Paleoproterozoic. Arch. Protist. 148:329-341. http://dx.doi.org/10.1016/S0003-9365(97)80013-9.
    • (1997) Arch. Protist , vol.148 , pp. 329-341
    • Wright, A.-D.1    Lynn, D.H.2
  • 24
    • 2442510059 scopus 로고    scopus 로고
    • Improved extraction of PCR-quality community DNA from digesta and fecal samples
    • Yu Z, Morrison M. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36:808-812.
    • (2004) Biotechniques , vol.36 , pp. 808-812
    • Yu, Z.1    Morrison, M.2
  • 27
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S, Wunsch C. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453. http://dx.doi.org/10.1016/0022-2836(70)90057-4.
    • (1970) J. Mol. Biol , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 28
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. http://dx.doi.org/10.1093/bioinformatics/btr381.
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1    Haas, B.J.2    Clemente, J.C.3    Quince, C.4    Knight, R.5
  • 30
    • 0000803388 scopus 로고
    • On population frequencies of species and the estimation of population parameters
    • Good IJ. 1953. On population frequencies of species and the estimation of population parameters. Biometrika 40:237-264. http://dx.doi.org/10.2307/2333344.
    • (1953) Biometrika , vol.40 , pp. 237-264
    • Good, I.J.1
  • 31
    • 33646876613 scopus 로고    scopus 로고
    • Entropy and diversity
    • Jost L. 2006. Entropy and diversity. Oikos 113:363. http://dx.doi.org/10.1111/j.2006.0030-1299.14714.x.
    • (2006) Oikos , vol.113 , pp. 363
    • Jost, L.1
  • 32
    • 0344898137 scopus 로고    scopus 로고
    • Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample
    • Chao A, Shen T-J. 2003. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ. Ecol. Stat. 10:429-443. http://dx.doi.org/10.1023/A:1026096204727.
    • (2003) Environ. Ecol. Stat , vol.10 , pp. 429-443
    • Chao, A.1    Shen, T.-J.2
  • 34
    • 84905903894 scopus 로고
    • The rumen ciliate fauna of cattle and sheep in Finnish Lapland, with special reference to the species regarded as specific to reindeer
    • Westerling B. 1969. The rumen ciliate fauna of cattle and sheep in Finnish Lapland, with special reference to the species regarded as specific to reindeer. Nord Vet. Med. 21:14-19.
    • (1969) Nord Vet. Med. , vol.21 , pp. 14-19
    • Westerling, B.1
  • 35
    • 0006371598 scopus 로고
    • Neue parasitische Infusorien aus dem Magen des Renntieres (Rangifer tarandus)
    • Dogiel VA. 1925. Neue parasitische Infusorien aus dem Magen des Renntieres (Rangifer tarandus). Arch. Rus. Protistol. 4:43-65.
    • (1925) Arch. Rus. Protistol. , vol.4 , pp. 43-65
    • Dogiel, V.A.1
  • 37
    • 0006283055 scopus 로고
    • Ophryoscolecidae (ciliata: entodiniomorphida) of the reindeer (Rangifer tarandus l ) from the Canadian arctic. ii. Diplodiniinae
    • Lubinsky G. 1957. Ophryoscolecidae (ciliata: entodiniomorphida) of the reindeer (Rangifer tarandus l.) from the Canadian arctic. ii. Diplodiniinae. Can. J. Zool. 36:927-959.
    • (1957) Can. J. Zool. , vol.36 , pp. 927-959
    • Lubinsky, G.1
  • 38
    • 0002288541 scopus 로고
    • Rumen ciliate fauna of semi-domestic reindeer (Rangifer tarandus t.) in Finland: composition, volume and some seasonal variations
    • Westerling B. 1970. Rumen ciliate fauna of semi-domestic reindeer (Rangifer tarandus t.) in Finland: composition, volume and some seasonal variations. Acta Zool. Fenn. 127:1-76.
    • (1970) Acta Zool. Fenn. , vol.127 , pp. 1-76
    • Westerling, B.1
  • 39
    • 0040208534 scopus 로고
    • Characterization studies on rumen bacteria isolated from Alaskan reindeer (Rangifer rarandus L.)
    • Luick JR (ed), Institute of Arctic Biology, Fairbanks, AK
    • Dehority BA. 1975. Characterization studies on rumen bacteria isolated from Alaskan reindeer (Rangifer rarandus L.), p 228-240. In Luick JR (ed), Proc. 1st Int. Reindeer Caribou Symp. Institute of Arctic Biology, Fairbanks, AK.
    • (1975) Proc. 1st Int. Reindeer Caribou Symp , pp. 228-240
    • Dehority, B.A.1
  • 40
    • 84867102451 scopus 로고    scopus 로고
    • Protozoa and digestive tract parameters in blue wildebeest (Connochaetes taurinus) and black wildebeest (Connochaetes gnou), with description of Entodinium taurinus n. sp
    • Booyse DG, Dehority BA. 2012. Protozoa and digestive tract parameters in blue wildebeest (Connochaetes taurinus) and black wildebeest (Connochaetes gnou), with description of Entodinium taurinus n. sp. Eur. J. Protistol. 48:283-289. http://dx.doi.org/10.1016/j.ejop.2012.04.004.
    • (2012) Eur. J. Protistol , vol.48 , pp. 283-289
    • Booyse, D.G.1    Dehority, B.A.2
  • 41
    • 0026916042 scopus 로고
    • Ciliate protozoa in the rumen of Kafue lechwe, Kobus leche kafuensis, in Zambia, with the description of four new species
    • Imai S, Tsutsumi Y, Yumara S, Mulenga A. 1992. Ciliate protozoa in the rumen of Kafue lechwe, Kobus leche kafuensis, in Zambia, with the description of four new species. J. Protozool. 39:564-572. http://dx.doi.org/10.1111/j.1550-7408.1992.tb04852.x.
    • (1992) J. Protozool , vol.39 , pp. 564-572
    • Imai, S.1    Tsutsumi, Y.2    Yumara, S.3    Mulenga, A.4
  • 42
    • 0016709521 scopus 로고
    • Rumen ciliates of the Tsessebe (Damaliscus lunatus lunatus) in South Africa
    • Van Hoven W. 1975. Rumen ciliates of the Tsessebe (Damaliscus lunatus lunatus) in South Africa. J. Eukaryot. Microbiol. 22:457-462.
    • (1975) J. Eukaryot. Microbiol. , vol.22 , pp. 457-462
    • Van Hoven, W.1
  • 43
    • 79952812637 scopus 로고    scopus 로고
    • The occurrence of the hindgut ciliate Hemiprorodon gymnoposthium (Ciliophora: Buetschliidae) from domestic horses in Cyprus
    • (In Turkish.)
    • Gürelli G, Göçmen B. 2010. The occurrence of the hindgut ciliate Hemiprorodon gymnoposthium (Ciliophora: Buetschliidae) from domestic horses in Cyprus. Turkiye Parazitol. Derg. 34:206 -208. (In Turkish.)
    • (2010) Turkiye Parazitol. Derg. , vol.34 , pp. 206-208
    • Gürelli, G.1    Göçmen, B.2
  • 44
    • 84861741429 scopus 로고    scopus 로고
    • Intestinal ciliate composition found in the feces of racing horses from Izmir
    • Gürelli G, Göçmen B. 2012. Intestinal ciliate composition found in the feces of racing horses from Izmir, Turkey. Eur. J. Protistol. 48:215-226. http://dx.doi.org/10.1016/j.ejop.2012.01.002.
    • (2012) Turkey. Eur. J. Protistol , vol.48 , pp. 215-226
    • Gürelli, G.1    Göçmen, B.2
  • 45
    • 0018487630 scopus 로고
    • Scanning electron microscopy of ciliary zones of the ciliate protozoa in the large intestine of the horse
    • Imai S, Ozeki K, Fujita J. 1979. Scanning electron microscopy of ciliary zones of the ciliate protozoa in the large intestine of the horse. J. Parasitol. 65:434-440. http://dx.doi.org/10.2307/3280291.
    • (1979) J. Parasitol , vol.65 , pp. 434-440
    • Imai, S.1    Ozeki, K.2    Fujita, J.3
  • 46
    • 3042763017 scopus 로고    scopus 로고
    • Phylogeny and biogeography of the "Australian" trichostomes (Ciliophora: Litostomata)
    • Cameron SL, O'Donoghue PJ. 2004. Phylogeny and biogeography of the "Australian" trichostomes (Ciliophora: Litostomata). Protist 155:215- 235. http://dx.doi.org/10.1078/143446104774199600.
    • (2004) Protist , vol.155 , pp. 215-235
    • Cameron, S.L.1    O'Donoghue, P.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.