Development of nucleic acid based techniques and possibilities of their application to rumen microbial ecology research

Journal of Animal and Feed Sciences

Volumn 20, Issue 3, 2011, Pages 315-337

  Pers Kamczyc, E ^a   Zmora, P ^a   Cieslak, A ^a   Szumacher Strabel, M ^a  

^a POZNA UNIVERSITY OF LIFE SCIENCES   (Poland)

Author keywords

Fish; Microorganisms; Molecular techniques; PCR DGGE; Real time PCR; Rumen

Indexed keywords

EID: 80053970577     PISSN: 12301388     EISSN: None     Source Type: Journal    
DOI: 10.22358/jafs/66189/2016     Document Type: Article

References (93)

1. Amann R., Binder B.J., Olson R.J., Chisholm S., Devereux R., Stahl D.A., 1990b. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919-1925 (Pubitemid 20202165)
2. Amann R., Krumholtz L., Stahl D.A., 1990a. Fluorescent oligonucleotide pro bing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172, 762-770 (Pubitemid 20070387)
3. Amann R.I., Ludwig W., Schleifer H.H., 1995. Phylogenetic identification and in situ detection of individual microbial cells without incubation. Microbiol. Rev. 59,143-169
4. Amor K.B., Vaughan E.F., de Vos W.M., 2007. Advanced molecular tools for the identification of lactic acid bacteria. J. Nutr. 137, 741-747
5. Baudart J., Lebaron P., 2010. Rapid detection of E. coli in waters using fluorescent in situ hybridization, direct viable counting and solid phase cytometry. J. Appl. Microbiol. 109,1253-1264
6. Bekele A.Z., Koike S., Kobayashi Y., 2010. Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. FEMS Microbiol. Lett. 305, 49-57
7. Boguhn J., Neumann D., Helm A., Strobel E., Tebbe C.C., Danicke S., Rodehutscord M., 2010. Effects of concentrate proportion in the diet with or without Fusarium toxin-contaminated triticale on ruminal fermentation and the structural diversity of rumen microbial communities in vitro. Arch. Anim. Nutr. 64, 467-483
8. Bustin S.A., 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25, 169-193
9. Campbell J.H., Clark J.S., Zak J.C., 2009. PCR-DGGE Comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan desert elevational gradient. Microbial Ecol. 57,261-266
10. Chaudhary P.P., Sirohi S.K., Kumar S., 2011. Improved extraction of quality DNA from methanogenic archaea present in rumen liquor for PCR application. Asian J. Anim. Sci. 5, 166-174
11. Chen T., Yuan J., Feng X., Wei H., Hua W., 2011. Effects of enrofloxacin on the human intestinal microbiota in vitro. Int. J. Antimicrobial Agents 37, 567-571
12. Cieslak A., Varadyova Z., KiSidayova S., Szumacher-Strabel M., 2009a. The effects of linoleic acid on the fermentation parameters, population density, and fatty acid profile of two rumen ciliate cultures, Entodinium caudatum and Diploplastron affine. Acta Protozool. 48, 51-61
13. Cieslak A., Zmora P., Nowakowska A., Szumacher-Strabel M., 2009b. Limonene affect rumen methanogenesis inhibiting the methanogens populations. Acta Biochim. Pol. 56, Suppl. 2, 59-60
14. Cikos S., Koppel J., 2009. Transformation of real-time PCR fluorescence data to target gene quantity. Anal. Biochem. 384, 1-10
15. Deng W., Xi D., Mao H., Wanapat M., 2008. The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review. Mol. Biol. Rep. 35, 265-274 (Pubitemid 351713258)
16. Denman S.E., McSweeney C.S., 2006. Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol. Ecol. 58, 572-582 (Pubitemid 44748164)
17. Ercolini D., 2004. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Meth. 56, 297-314 (Pubitemid 38210334)
18. Ercolini D., Hill P.J., Dodd C.E.R., 2003. Bacterial community structure and location in Stilton cheese. Appl. Environ. Microbiol. 69, 3540-3548 (Pubitemid 36693365)
19. Fischer S.G., Lerman L., 1983. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Nat. Acad. Sci. USA 80, 1579-1583 (Pubitemid 13052453)
20. Fisher M.M., Triplett E.W., 1999. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65, 4630-4636
21. Freitas K.C., Gabriel J.E., Leite L.C., Dutra de Armas R., Lanna D.P.D., Madeira H.M.F., 2008. Molecular characterization of ruminal bacterial diversity in vitro. Acta Sci. Anim. Sci. 30, 187-192
22. Garcia J.L., Patel B.K.C., Ollivier B., 2000. Taxonomic, phylogenetic, and ecological diversity of methanogenic. Archaea. Anaerobe 6, 205-226 (Pubitemid 30604012)
23. Graeme T.,Attwood G.T., Klieve A.V., Ouwerkerk D., Patel B.K.C., 1998. Ammonia-hyperproducing bacteria from New Zealand ruminants. Appl. Environ. Microbiol. 64, 1796-1804 (Pubitemid 28234786)
24. Guan L.L., Nkrumah J.D., Basarab J.A., Moore S.S., 2008. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency. FEMS Microbiol. Lett. 288,85-91
25. Haferlach C, Bacher U., 2011. Cytogenetic methods in chronic lymphocytic leukemia. Methods Mol. Biol. 730, 119-130
26. Hemandez-Sanabria E., Guan L.L., Goonewardene L.A., Li M., Mujibi D.F., Stothard P., Moore S.S., Leon-Quintero M.C., 2010. Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits. Appl. Environ. Microbiol. 76, 6338-6350
27. Hespell R.B., Akin D.E., Dehority B.A., 1997. Bacteria, fungi and protozoa of the rumen. In: R.I. Mackie, B.A. White, R.E. Isaacson (Editors). Gastrointestinal Microbes and Host Interactions: Gastrointestinal Microbiology. Chapman and Hall, Vol. 2, pp. 85-89
28. Jackson C.R., Roden E.E., Churchill P.F., 2000. Denaturing gradient gel electrophoresis can fail to separate 16S rDNA fragments with multiple base differences. Mol. Biol. Today 1,49-51
29. Jupraputtasri W, Boonapatcharoen N., Cheevadhanarak S., Chaiprasert P., Tanticharoen M., Techkarnjanaruk S., 2005. Use of alternative Archaea-specific probe for methanogen detection. J. Microbiol. Meth. 61,95-104 (Pubitemid 40164879)
30. Karnati S.K.R., Sylvester J.T., Ribeiro C.V.D.M., Gilligan L.E., Firkins J.L., 2009. Investigating unsaturated fat, monensin, or bromoethanesulfonate in continuous cultures retaining ruminal protozoa. I. Fermentation, biohydrogenation, and microbial protein synthesis. J. Dairy Sci. 99, 3849-3860
31. Khejornsart P., Wanapat M., 2010. Effect of chemical treatment of rice straw on rumen fermentation characteristic, anaerobic fungal diversity in vitro. J. Anim. Vet. Adv. 9, 3070-3076
32. Kittelmann S., Janssen P.H., 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
33. Klieve A.V., Hennessy D., Ouwerkerk D., Forster R.J., Mackie R.I., Attwood G.T., 2003. Establishing populations of Megasphaera elsdenii YE 34 and Butyrivibrio fibrisolvens YE 44 in the rumen of cattle fed high grain diets. J. Appl. Microbiol. 95, 621-630 (Pubitemid 37041095)
34. Kocherginskaya S., Aminov R.I., White B.A., 2001. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 7, 119-134 (Pubitemid 32928200)
35. Koike S., Kobayashi Y., 2001. Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol. Lett. 204, 361-366 (Pubitemid 33145280)
36. Koike S., Kobayashi Y., 2009. Fibrolytic rumen bacteria: their ecology and functions. Asian- Austr. J.Anim. Sci.22, 131-138
37. Krause D.O., Russell J.B., 1996. How many nominal bacteria are there? J. Dairy Sci. 79, 1467- 1475. (Pubitemid 126429190)
38. Leng J., Zhong X., Zhu R.J., Yang S.L., Gou X., Mao H.M., 2011. Assessment of protozoa in Yunnan Yellow Cattle rumen based on the 18S rRNA sequences. Mol. Biol. Rep. 38, 577-585
39. Li Y., Kul C.Y.S., Xu J., Saxena D., Caufield P.W., 2005. Survey of oral microbial diversity using pcr-based denaturing gradient gel electrophoresis. J. Dent. Res. 84, 559-564 (Pubitemid 43827865)
40. Liu W.T., Marsh T.L., Cheng H., Forney L.J., 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63,4516-4522 (Pubitemid 27485783)
41. Lloyd D., Williams A.G., Amann R., Hayes A.J., Durrant L., Ralphs J.R., 1996. Intracellular prokaryotes in rumen ciliates protozoa: detection by confocal laser scanning microscopy after in situ hybridization with fluorescent 16S rRNA probes. Eur. J. Protistol. 32, 523-531 (Pubitemid 27049954)
42. Lukas F., Simunek J., Mrazek J., Kopecny J., 2010. PCR-DGGE analysis of bacterial population attached to the bovine rumen wall. Folia Microbiol. Prague 55, 345-348
43. Lwin K.O., Hayakawa M., Ban-Tokuda T., Matsui H., 2011. Real-time PCR assays for monitoring anaerobic fungal biomass and population size in the rumen. Curr. Microbiol. 62, 1147-1151
44. MacKay I.M. (Editor), 2007. Real-time PCR in Microbiology: From Diagnosis to Characterization. Caister Academic Press
45. Mackie R.I., Aminov R.I., Hu W., Klieve A.V., Ouwerkerk D., Sundset M.A., Kamagata Y, 2003. Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl. Environ. Microbiol. 69, 6808-6815 (Pubitemid 37420221)
46. Makkar H.P.S., McSweeney C.S. (Editors), 2005. Methods in Gut Microbial Ecology for Ruminants. IAEA, pp. 3-19
47. Mao S.Y, Zhang G., Zhu W.Y., 2008. Effect of disodium fumarate on ruminal metabolism and rumen bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA. FEMS Microbiol. Ecol. 140, 293-306
48. Marteau P., Pochart P., Dore J., Bera-Maillet C, Bernalier A., CorthierG., 2001. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl. Environ. Microbiol. 67, 4939-4942 (Pubitemid 33646136)
49. McCracken V.J., Simpson J.M., Mackie R.I., Gaskins H.R., 2001. Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota. J. Nutr. 131, 1862-1870 (Pubitemid 32520459)
50. Melo J.B., Backx L., Vermeesch J.R., Santos H.G., Sousa A.C., Kosyakova N., Weise A., von Eggeling F., Liehr T., Carreira I.M., 2011. Chromosome 5 derived small supernumerary marker: towards a genotype/phenotype correlation of proximal chromosome 5 imbalances. J. Appl. Genet. 52, 25-32
51. Muyzer G., de Waal E.C., Uitterlinden A.G., 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700 (Pubitemid 23072343)
52. Narihiro T., TeradaT., Ohashi A., Wu J.H., Liu W.T., Araki N., Kamagata Y, Nakamura K., Sekiguchi Y, 2009. Quantitative detection of culturable methanogenic Archara abundance in anaerobic treatment systems Rusing the sequence-specific rRNA cleavage metod. ISME J. 3, 522-535
53. Nicholson M.J., Evans P.N., Joblin K.N., 2007. Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microbial Ecol. 54,141-150 (Pubitemid 47036691)
54. Omar K.B., Barnard T.G., Jagals P., 2010. Development of a competitive PCR assay for the quantification of total Escherichia coli DNA in water. Afr. J. Biotechnol. 9, 564-572
55. Ouwerkerk D., Klieve A.V., Forster R.J., 2002. Enumeration of Megasphaera elsdenii in rumen contents by real-time Taq nuclease assay. J. Appl. Microbiol. 2, 753-758 (Pubitemid 34437905)
56. Perumbakkam S., Craig A.M., 2011. Design and in vitro evaluation of new rpoB-DGGE primers for ruminants. FEMS Microbiol. Ecol. 76, 156-169
57. Pfaffl M.W., 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucl. Acid. Res. I,29:e45
58. Raskin L., Stromley J.M., Rittmann B.E., Stahl D.A., 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60, 1232- 1240 (Pubitemid 24113941)
59. Regensbogenova M., Pristas P., Javorsky P., Moon-van der Staay S. Y., van der Staay G.W., Hackstein J.H., Newbold C.J., McEwan N.R., 2004. Assessment of ciliates in the sheep rumen by DGGE. Lett. Appl. Microbiol. 39, 144-147 (Pubitemid 39036979)
60. Reilly K., Attwood G.T., 1998. Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl. Environ. Microbiol. 64, 907-913 (Pubitemid 28108464)
61. Sadet S., Martin C, Meunier B., Morgavi D.P., 2007. PCR-DGGE analysis reveals a distinct diversity in the bacterial population attached to the rumen epithelium. Animal 1, 939-944 (Pubitemid 47236822)
62. Sekhavati M.H., Mesgaran M.D., Nassiri M.R., Mohammadabadi T., Rezaii F., Fani Maleki F., 2009. Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal population s in both in vitro and in vivo systems. Mycol. Res. 113, 1146-1153
63. Sheffield V.C., Cox D.R., Lerman L.S., Myers R.M., 1989. Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Nat. Acad. Sci. USA 86, 232-236 (Pubitemid 19036361)
64. Shin E.C., Cho K.M., Lim W.J., Hong S.Y, An C.L., Kim Y.K., Choi B.R., An J.M., Kang J.M., Kim H., Yun H.D., 2004. Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences. J. Appl. Microbiol. 97, 378-383 (Pubitemid 38998670)
65. Simpson J.M., McCracken V.J., Gaskins H.R., Mackie R.I., 2000. Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl. Environ. Microbiol. 66, 4705-4714
66. Simpson J.M., McCracken V.J., White B.A., Gaskins H.R., Mackie R.I., 1999. Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. J. Microbiol. Meth. 36, 167-179 (Pubitemid 29222041)
67. Simpson JM, Martineau B, Jones WE, Ballam JM, Mackie RI. 2002. Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber. Microbial. Ecol. 44, 186-197 (Pubitemid 36941386)
68. Singh K.M., Tripathi A.K., Pandya P.R., Rank D.N., Kothari R.K., Joshi C.G., 2011. Dasytricha dominance in surti buffalo rumen revealed by 18S rRNA sequences and real-time PCR assay. Curr. Microbiol. doi:10.1007/s00284-011-9975- 4
69. Stabnikova O., Liu X.Y., Wang J.Y, Ivanov V., 2006. Quantification of methanogens by fluorescence in situ hybridization with oligonucleotide probe. Appl. Microbiol. Biotechnol. 73, 696-702 (Pubitemid 44748961)
70. Stahl D.A., Amann R.I., 1990. Development and application of nucleic acid probes in bacterial systematics. In: E. Stackebrandt, M. Goodfellow (Editors). Nucleic Acid Techniques in Bacterial Systematics. John Wiley, pp. 205-248
71. Stewart C.S., Flint H.J., Bryant M.P., 1997. The rumen bacteria. In: P.N. Hobson, C.S. Stewart (Editors). The Rumen Microbial Ecosystem. 2nd Edition. Springer, pp. 49-55
72. Sylvester J.T., Kamati S.K.R., Yu Z., Morrison M., Firkins J.L., 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J. Nutr. 134, 3378-3384 (Pubitemid 39603012)
73. Szumacher-Strabel M., Cieslak A., 2010. Potential of phytofactors to mitigate rumen ammonia and methane production. J. Anim. Feed Sci. 19, 329-348
74. Szumacher-Strabel M., Cieslak A., Nowakowska A., 2009. Effect of oils rich in linoleic acid on in vitro rumen fermentation parameters of sheep, goats and dairy cows. J. Anim. Feed Sci. 18, 440-452
75. Szumacher-Strabel M., Zmora P., Roj E., Stochmal A., Pers-Kamczyc E., Urbanczyk A., Oleszek W., Lechniak D., Cieslak A., 2011. The potential of the wild dog rose (Rosa canina) to mitigate in vitro rumen methane. J. Anim. Feed Sci. 20, 285-299
76. Tajima K., Aminov R.I., Nagamine T., Matsui H., Nakamura M., Benno Y, 2001. Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl. Environ. Microbiol. 67, 2766-2774 (Pubitemid 33639756)
77. Tatsuoka N., Mohammed N., Mitsumori M., Tajima K., Hara K., Kurihara M., Itabashi H., 2007. Analysis of methanogens in the bovine rumen by polymerase chain reaction single-strand conformation polymorphism. Anim. Sci. J. 78, 512-518 (Pubitemid 47373586)
78. Tay T.L.S., Ivanov V., Kim I.S., Feng L., Tay J.H., 2001. Quantification of ratios of Bacteria and Archaea in methanogenic microbial community by fluorescence in situ hybridization and fluorescence spectrometry. World J. Microbiol. Biotechnol. 17, 583-589 (Pubitemid 33082896)
79. Temmerman R., Masco L., Vanhoutte T., Huys G., Swings J., 2003. Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities. Appl. Environ. Microbiol. 69, 6380-6385 (Pubitemid 37420166)
80. Vaughan E.E., Heilig H.G.H.J., Zoetendal E.G., Satokari R., Collins J.K., Akkermans A.D.L., de Vos W.M., 1999. Molecular approaches to study probiotic bacteria. Trends Food Sci. Technol. 10,400-404
81. Wagner M., Horn M., Daims H., 2003. Fluorescence in situ hybridization for the identification and characterization of prokaryotes. Curr. Opin. Microbiol. 6, 302-309 (Pubitemid 36841675)
82. Weimer P.J., Waghorn G.C., Odt C.L., Mertens D.R., 1999. Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J. Dairy Sci. 82,122-134 (Pubitemid 129552325)
83. Wright A.D., Auckland C.H., Lynn D.H., 2007. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl. Environ. Microbiol. 73, 4206-4210 (Pubitemid 47068159)
84. Wu Q., Zhao X.H., Zhao S.Y., 2006. Application of PCR-DGGE in research of bacterial diversity in drinking water. Biomed. Environ. Sci. 19, 371-374 (Pubitemid 44916214)
85. Yanagita K., Kamagata Y, Kawaharasaki M., Suzuki T., Nakamura Y, Minato H., 2000. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci. Biotechnol. Biochem. 64, 1737-1742
86. Yu Z., Garcia-Gonzalez R.,. Schanbacher F.L, Morrison M.. 2008. Evaluation of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaeaspecific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 74, 889-893. (Pubitemid 351225744)
87. Yu Z.T., Morrison M., 2004a. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70, 4800-4806 (Pubitemid 39095507)
88. Yu Z.T., Morrison M., 2004b. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808-812 (Pubitemid 38620199)
89. Zhang T, Fang H.H., 2006. Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl. Microbiol. Biotechnol. 70,281-289 (Pubitemid 43345152)
90. Zheng D., Raskin L., 2000. Quantification of Methanosaeta species in anaerobic bioreactors using genus- and species-specific hybridization probes. Microbial Ecol. 39, 246-262 (Pubitemid 30454200)
91. Zhou M., Hernandez-Sanabria E., Guan le L., 2010. Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis. Appl. Environ. Microbiol. 76,3776-3786
92. Zoetendal E.G., Akkermans A.L., Devos W.M., 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64, 3854-3859 (Pubitemid 28462983)
93. Zoetendal E.G., Collier C.T., Koike S., Mackie R.I., Gaskins H.R., 2004. Molecular ecological analysis of the gastrointestinal microbiota: A review. J. Nutr. 134, 465-472 (Pubitemid 38141834)