Design and use of 16S ribosomal DNA-directed primers in competitive PCRs to enumerate proteolytic bacteria in the rumen

Microbial Ecology

Volumn 43, Issue 2, 2002, Pages 259-270

  Reilly, K ^a,c   Carruthers, V R ^b,d   Attwood, G T ^a  

^a AGRESEARCH GRASSLANDS   (New Zealand)

^b Dexcel Limited   (New Zealand)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d DEPARTMENT OF CONSERVATION   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; RUMEN;

BACTERIA (MICROORGANISMS); BOS TAURUS; BUTYRIVIBRIO FIBRISOLVENS; EUBACTERIUM SP.; PREVOTELLA BRYANTII; STREPTOCOCCUS;

BACTERIAL DNA; NITROGEN; PRIMER DNA; RNA 16S;

ANIMAL; ANIMAL FOOD; ARTICLE; CARBOHYDRATE DIET; CATTLE; EUBACTERIUM; FEMALE; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; POLYMERASE CHAIN REACTION; PREVOTELLA; RUMINANT STOMACH; STREPTOCOCCUS;

ANIMAL FEED; ANIMALS; CATTLE; DIETARY CARBOHYDRATES; DNA PRIMERS; DNA, BACTERIAL; EUBACTERIUM; FEMALE; NITROGEN; POLYMERASE CHAIN REACTION; PREVOTELLA; RNA, RIBOSOMAL, 16S; RUMEN; STREPTOCOCCUS;

EID: 0036490051     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-001-1052-2     Document Type: Article

References (45)

1. Abou Akkada AR, Blackburn TH (1963) Some observations on the nitrogen metabolism of rumen proteolytic bacteria. J Gen Microbiol 31:461-469
2. Attwood GT, Reilly K (1995) Identification of proteolytic rumen bacteria isolated from New Zealand cattle. J Appl Bacteriol 79:22-29
3. Attwood GT, Reilly K (1996) Characterization of proteolytic activities of rumen bacterial isolates from forage-fed cattle. J Appl Bacteriol 81:545-552
4. Attwood GT, Reilly K, Patel BKC (1996) Clostridium proteoclasticum sp. nov., a novel proteolytic bacterium from the bovine rumen. Int J Syst Bacteriol 46:753-758
5. Avgustin G, Wallace RJ, Flint HJ (1997) Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola. Int J Syst Bacteriol 47:284-288
6. Avgustin G, Wright F, Flint HJ (1994) Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminicola from the rumen, Int J Syst Bacteriol 44:246-255
7. Blackburn TH, Hobson PN (1962) Further studies on the isolation of proteolytic bacteria from the sheep rumen. J Gen Microbiol 29:69-81
8. Brock FM, Forsberg CW, Buchanan-Smith JG (1982) Proteolytic activity of rumen microorganisms and effects of proteinase inhibitors. Appl Environ Microbiol 44:561-569
9. Brooker JD, O'Donovan LA, Skene I, Clarke K, Blackwell L, Musiera P (1994) Streptococcus caprinus sp. nov., a tannin-resistant ruminal bacterium from feral goats. Lett Appl Microbiol 18:313-318
10. Bryant MP, Robinson IM, Lindahl IL (1961) A note on the flora and fauna in the rumen of steers fed a feed lot bloat-provoking ration and the effect of penicillin. Appl Microbiol 9:511-515
11. Bryant MP, and Small N (1956) The anaerobic monotrichous butyric acid-producing curved rod-shaped bacteria of the rumen. J Bacteriol 72:16-21
12. Erwin ES, Marco SJ, Emery EM (1961) Volatile fatty acid analysis of blood and rumen fluid by gas chromatography. J Dairy Sci 44:1768-1771
13. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle,WA
14. Forster RJ, Gong J, Teather RM (1997) Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen. Appl Environ Microbiol 63:1256-1260
15. Forster RJ, Teather RM, Gong J, Deng S-J (1996) 16S rDNA analysis of Butyrivibrio fibrisolvens: phylogenetic position and relation to butyrate-producing anaerobic bacteria from the rumen of white-tailed deer. Lett Appl Microbiol 23:218-222
16. Fulghum RS, Moore WEC (1963) Isolation, enumeration, and characteristics of proteolytic ruminal bacteria. J Bacteriol 85:808-815
17. Hazlewood GP, Nugent JHA (1978) Leaf fraction 1 protein as a nitrogen source for the growth of a proteolytic rumen bacterium. J Gen Microbiol 106:369-371
18. Hazlewood GP, Orpin CG, Greenwood Y, Black ME (1983) Isolation of proteolytic rumen bacteria by use of selective medium containing leaf fraction 1 protein (ribulose bisphosphate carboxylase). Appl Environ Microbiol 45:1780-1784
19. Higginbottom C, Wheater DWF (1954) The incidence of Streptococcus boris in cattle. J Agric Sci 44:434-442
20. Holmes CW, Wilson GF (1987) Milk Production from Pasture. Butterworths Agricultural Books, Wellington, New Zealand pp 107-112.
21. Hungate RE (1950) The anaerobic mesophilic cellulolytic bacteria. Bacteriol Rev 14:1-49
22. Hungate RE (1957) Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289-311
23. Hungate RE (1966) The Rumen and Its Microbes. Academic Press, New York
24. Johns AT (1955) Pasture quality and ruminant digestion. 1. Seasonal change in botanical and chemical composition of pasture. NZ J Sci Technol A37:301-311
25. Jukes TH, Cantor CR (1969) Evolution of protein molecules In: HN Munro (ed) Mammalian Protein Metabolism, vol 3, Academic Press, New York pp 21-132.
26. Kobayashi Y, Forster RJ, Teather RM (2000) Development of a competitive polymerase chain reaction assay for the ruminal bacterium Butyrivibrio fibrisolvens OB156 and its use for tracking an OB156-derived recombinant. FEMS Microbiol Lett 188:185-190
27. Leedle JAZ, Hespell RB (1980) Differential carbohydrate media and anaerobic replica plating technique in delineating carbohydrate utilizing subgroups in rumen bacterial populations. Appl Environ Microbiol 39:709-719
28. MacRae JC, Ulyatt MJ (1974) Quantitative digestion of flesh herbage by sheep. II. The sites of digestion of some nitrogenous constituents. J Agric Sci (Camb) 82:309-319
29. Maidak BL, Lilburn TG, Parker Jr CT, Saxman PR, Farris RJ Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project) Nucleic Acids Res 29:173-174
30. Nelms LF, Odelson DA, Whitehead TR, Hespell RB (1995) Differentiation of ruminal and human Streptococcus bovis strains by DNA homology and 16S rRNA probes. Curr Microbiol 31:294-300
31. Nugent JHA, Mangan JL (1981) Characteristics of the rumen proteolysis of fraction I (18S) leaf protein from lucerne (Medicago saliva L). Brit J Nutrit 46:39
32. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comp Applicat Biosci 12:357-358
33. Piatak M, Luk KC, Williams B, Lifson JD (1993) Quantitative competitive polymerase chain reaction for accurate quantitation of HIV DNA and RNA species. BioTechniques 14:70-80
34. Prins RA, van Rheenen DL, van't Klooster AT (1983) Characterization of microbial proteolytic enzymes in the rumen. Ant van Leeuwen 49:585-595
35. Reilly K, Attwood GT (1998) Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl Environ Microbiol 64:907-913
36. Russell JB, Cook GM (1995) Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol Rev 59:48-62
37. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
38. Shah HN, Collins MD (1990) Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol 40:205-208
39. Van Gylswyk NO (1990) Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass silage-based diets. FEMS MiCrobiol Ecol 73:243-254
40. Wallace RJ, Brammall ML (1985) The role of different species of bacteria in the hydrolysis of protein in the rumen. J Gen Microbiol 131:821-832
41. Wallace RJ, Broderick GA, Brammall ML (1987) Microbial protein and peptide metabolism in rumen fluid from faunated and ciliate-free sheep. Brit J Nutrit 58:87-93
42. Wallace RJ, Broderick GA, Brammall ML (1987) Protein degradation by ruminal microorganisms from sheep fed dietary supplements of urea, casein or albumin. Appl Environ Microbiol 53:751-753
43. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703
44. Whitford MF, Lanke LJ, Forster RJ, and Teather RM (2001) Lachnobacterium bovis gen. nov; sp. a novel bacterium isolated from the rumen and faeces of cattle. Int J Syst Evol Microbiol 51:1977-1981
45. Willems A, Amat-Marco M, Collins MD (1996) Phylogenetic analysis of Butyrivibrio strains reveals three distinct groups of species within the Clostridium subphylum of the gram-positive bacteria. Int J Syst Bacteriol 46:195-199