Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems

Mycological Research

Volumn 113, Issue 10, 2009, Pages 1146-1153

  Sekhavati, Mohammad H ^a   Mesgaran, Mohsen Danesh ^a   Nassiri, Mohammad R ^a   Mohammadabadi, Tahereh ^b   Rezaii, Farkhondeh ^a   Fani Maleki, Adham ^a  

^a FERDOWSI UNIVERSITY OF MASHHAD   (Iran)

^b Ramin Agricultural and Natural Resources University Ahwaz   (Iran)

Author keywords

Chitin; Non structural carbohydrate; QC PCR; Rumen anaerobic fungi

Indexed keywords

BIOASSAY; BIOMASS; CARBOHYDRATE; CHITIN; FUNGUS; POLYMERASE CHAIN REACTION; RUMINANT;

ANAEROBIC GROWTH; ANIMAL; ANIMAL FOOD; ARTICLE; BIOLOGICAL MODEL; BIOMASS; EVALUATION; FUNGUS; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MALE; METABOLISM; METHODOLOGY; MICROBIOLOGY; POLYMERASE CHAIN REACTION; RUMINANT STOMACH; WHEAT;

ANAEROBIOSIS; ANIMAL FEED; ANIMALS; BIOMASS; FUNGI; MALE; MODELS, BIOLOGICAL; POLYMERASE CHAIN REACTION; RUMEN; TRITICUM;

FUNGI; TRITICUM AESTIVUM;

EID: 70350780203     PISSN: 09537562     EISSN: 14698102     Source Type: Journal    
DOI: 10.1016/j.mycres.2009.07.017     Document Type: Article

References (47)

1. Akin D.E., Ames Gottferd N., Hartly R.D., Fulcher R.G., and Rigsby C.L. Micro-spectrometry of phenolic compounds in Bermuda grass cell walls in relation to microbial digestion. Crop Science 30 (1990) 396
2. Bauchop T. Rumen anaerobic fungi of cattle and sheep. Journal of Applied Environmental Microbiology 38 (1979) 148-158
3. Boom R., Sol C.J.A., Salimans M.M.M., Jason C.L., Wertheim-Van Dillen P.M.E., and Van Der Noordaa J. Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28 (1990) 495-503
4. Bowman B.H., Taylor J.W., Brownlee A.G., Lee J., Lu S.D., and Withe T.J. Molecular evolution of the fungi: relationship of the basidiomycetes, ascomycetes, and chytridiomycetes. Journal of Molecular Biology Evolution 9 (1992) 285-296
5. Brookman J.L., and Nicholson M.J. In: Makkar H.P.S., and McSweeney C.S. (Eds). 4.3 Anaerobic Fungal Populations. Methods in Gut Microbial Ecology for Ruminants (2005), Springer, Dordrecht 139-150
6. Chen G.C., and Johnson B.R. Improved colorimetric determination of cell wall chitin in wood decay fungi. Applied and Environmental Microbiology 46 (1983) 13-16
7. Degraves F.J., Gao D., and Kaltenboeck T. High-sensitivity quantitative PCR platform. BioTechniques 34 (2003) 106-115
8. Dehority B.A., and Orpin C.G. Development of, and natural fluctuations in, rumen microbial populations. In: Hobson P.N., and Stewart C.S. (Eds). The Rumen Microbial Ecosystem (1997), Elsevier, London 196-245
9. Dehority B.A., and Tirabasso P.A. Effect of feeding frequency on bacterial and fungal concentrations, pH, and other parameters in the rumen. Journal of Animal Science 79 (2001) 2908-2912
10. Denman S.E., and McSweeney C.S. Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiology Ecology 58 (2006) 572-582
11. Dieffenbach C.W., and Dveksler G.S. PCR Primer. 2nd edn (2003), Cold Spring Harbor, New York
12. Edwards J.E., Kingston-Smith A.H., Jimenez H.R., Huws S.A., Skøt K.P., Griffith G.W., McEwan N.R., and Theodorou M.K. Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen. FEMS Microbiology Ecology 66 (2008) 537-545
13. El-Shazly K., Dehority B.A., and Johnson R.R. Effect of starch on the digestion of cellulose in vitro and in vivo by rumen microorganisms. Journal of Animal Science 20 (1961) 268
14. Fliegerova K., Mrazek J., and Voigt K. Differentiation of anaerobic polycentric fungi by rDNA PCR-RFLP. Folia Microbiology 51 (2006) 273-277
15. Franz W., Hlfriende H., and Thomas L. Quantification of mRNA expression by competitive PCR using non-homologous competitors containing a shifted restriction site. Nucleic Acids Research 29 (2001) 11, e52
16. Freeman W.M., Wallker S.J., and Vrana K.E. Quantification RT-PCR: pitfalls and potential. Gastrointestinal Microbiology (1999), Chapman and Hall, New York
17. Gaiger A., Henn T., Horth E., Geissler K., Mitterbauer G., Maier-Dobersberger T., Greinnix H., Mannhalter C., Hass O.A., Lechner K., and Lion T. Increase of bcr-abl chimeric mRNA expression in tumor cells of patients with chronic myeloid leukemia precedes disease progression. Blood 86 (1995) 2371-2378
18. Gay L. Chitin content and chitin syntheses activity as indicators of the growth of three different anaerobic rumen fungi. FEMS Microbiology Letters 80 (1991) 99
19. Grenet E., Fonty G., Jamot J., and Bonnemoy F. Influence of diet and monensin on development of anaerobic fungi in the rumen, duodenum, cecum, and faeces of cows. Applied and Environmental Microbiology 55 (1989) 2360-2364
20. Harms G., Layton A.C., Dionisi H.M., Garrett V.M., Hawkins S.A., Robinson K.G., and Sayler G.S. Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environed Science Technology 37 (2003) 343-351
21. Joblin K.N. Isolation, enumeration, and maintenance of rumen anaerobic fungi in roll tubes. Applied and Environmental Microbiology 49 (1981) 1119-1122
22. Kamra D.N., Saha Bhatt N., Chaudhart L.C., and Agarwal N. Effect of diet on enzyme profile, biochemical changes and in sacco degradability of feeds in the rumen of buffalo. Asian-Australian Journal of Animal Sciences 16 (2003) 374-379
23. Khezri A., Rezayazdi K., Danesh Mesgaran M., and Moradi-Sharbabak M. Effect of different rumen-degradable carbohydrates on rumen fermentation, nitrogen metabolism and lactation performance of Holstein dairy cows. Asian-Australian Journal of Animal Sciences 5 (2009) 651-658
24. Klaschik S.L., Lehmann A., Raadts A., Hoeft, and Stuber F. Comparison of different decontamination method for reagents to detect low concentrations of bacterial 16S DNA by real-time PCR. Molecular Biotechnology 22 (2002) 231-242
25. Lehninger A.L., Nelson D.L., and Cox M.M. Principle of Biochemistry. 2nd edn (1993), Worth Publishers
26. Lion T., Izraeli S., Henn T., Gaiger A., Mor W., and Gardaner H. Monitoring of residual disease in chronic myelogenous leukemia by quantities polymerase chain reaction. Leukemia 6 (1992) 495-499
27. Lowe S.E., Griffith G.W., Milne A., Theodorou M.K., and Trinci A.P. Life cycle and growth kinetics of an anaerobic rumen fungus. Journal of General Microbiology 133 (1987) 1815-1827
28. Mould F.L., Ørskov E.R., and Mann S.O. Associative effects of mixed feeds. I. Effects of type and level of supplementation and the influence of the rumen fluid pH on cellulolysis in vivo and dry matter digestion of various roughages. Animal Feed Science and Technology 10 (1983) 15-30
29. Mountfort D.O., and Asher R.A. Production and regulation of cellulase by two strains of the rumen anaerobic fungus Neocalliniastiv frontalis. Applied and Environmental Microbiology 49 (1985) 1314-1322
30. Obispo N.E., and Dehority B.A. A most probable number method for enumeration of rumen fungi with studies on factors affecting their concentration in the rumen. Journal of Microbiological Methods 16 (1992) 259-270
31. Orpin C.G. Studies in the rumen flagellate Neocallimastix frontalis. Journal of General Microbiology 5 (1975) 249-262
32. Orpin C.G. Anaerobic Fungi: taxonomy, biology, and distribution in nature. Anaerobic Fungi: biology, ecology and function (1994), Marcel Dekker, New York
33. Orpin C.G., and Letcher A.J. Utilization of cellulose, starch, xylan and other hemicelluloses for growth by the rumen phycomycete Neocallimastix frontalis. Current Microbiology 3 (1979) 121-124
34. Orpin C.G., and Greenwood Y. Nutritional and germination requirements of the rumen chytridiomycete Neocallimastix patriciarum. Transactions of the British Mycological Society 86 (1986) 103-109
35. The rumen anaerobic fungi. In: Orpin C.G., Joblin K.N., Hobson P.N., and Stewart C.S. (Eds). The Rumen Microbial Ecosystem. 2nd edn (1997), Chapman &Hall, New York 140-195
36. Orpin C.G., and Joblin K.N. The rumen anaerobic fungi. The Rumen Microbial Ecosystem (1988), Elsevier, Hobson, London Lehninger AL, Nelson DL, Cox MM, 1993. Principle of Biochemistry, 2nd edn. Worth Publishers
37. Phillips M.W., and Gordon G.L.R. Growth characteristics on cellobiose of three different anaerobic fungi isolated from the ovine rumen. Applied and Environmental Microbiology 55 (1989) 1695-1702
38. Piatak M., Luk K.C., Williams B., and Lifson J.D. Quantitative competitive polymerase chain reaction for accurate quantification of HIV DNA and RNA species. Journal of Biotechniques 14 (1993) 70-80
39. Rezaeian M, 1996. Assessment and distribution of anaerobic fungi in the ruminant gut. Ph.D. thesis, University of Newcastle Upon Tyne.
40. Rezaeian M., Beakes G.W., and Parker D.S. Methods for the isolation, culture and assessment of the status of anaerobic rumen chytrids in both in vitro and in vivo systems. Journal of Mycological Research 108 (2004) 1215-1226
41. Rezaeian M., Beakes G.W., and Chaudhry A.S. Relative fibrolytic activities of anaerobic rumen fungi on untreated and sodium hydroxide treated barley straw in in vitro culture. Anaerobe 11 (2005) 163-175
42. Roger V., Fonty G., Komisarczuk S., and Gouet P.H. Effects of physicochemical factors on the adhesion to cellulose Avicel of the ruminal bacteria Ruminococous flavefaciens and Fibrobacter succinogenes subsp. succinogenes. Applied and Environmental Microbiology 56 (1990) 3081-3087
43. Snedecor G.W., and Cochran W.G. Statistical Methods. 6th edn (1967), Iowa State University Press, Ames, Iowa, USA
44. Stahl D.A., Flesher B., Mansfield H.R., and Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Applied and Environmental Microbiology 54 (1988) 1079-1084
45. Theodorou M.K., Gill M., King-Spooner C., and Beever D.E. Enumeration of anaerobic chytridiomycetes as thallus-forming units: novel method for quantification of fibrolytic fungal populations from the digestive tract ecosystem. Applied and Environmental Microbiology 56 (1990) 1073-1078
46. Tichopal A., Didier A., and Pfaffl M.W. Inhibition of real-time PCR quantification due to tissue-specific contaminations. Molecular and Cell Probes 18 (2004) 45-50
47. Trinci A.P.J., Davies D.R., Gull K., Lawrence M.I., Nielsen B.B., Rickers A., and Theodorou M.K. Anaerobic fungi in herbivorous animals. Journal of Mycological Research 98 (1994) 129-152