Changes in ruminal microbiota due to rumen content processing and incubation in single-flow continuous-culture fermenters

Animal Production Science

Volumn 52, Issue 9, 2012, Pages 813-822

  Soto, E C ^a   Yanez Ruiz D R ^a   Cantalapiedra Hijar, G ^a   Vivas, A ^a   Molina Alcaide, E ^a  

^a CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ABUNDANCE; BACTERIUM; ELECTROKINESIS; FERMENTATION; FUNGUS; INOCULATION; METHANOGENESIS; MICROBIAL COMMUNITY; MICROBIOLOGY; POLYMORPHISM; SPECIES EVENNESS; SPECIES RICHNESS;

EID: 84865020896     PISSN: 18360939     EISSN: None     Source Type: Journal    
DOI: 10.1071/AN11312     Document Type: Article

References (59)

1. References AOAC (2005) 'Official methods of analysis.' 18th edn. (Association of Official Analytical Chemists: Gaithersburg, MD
2. Cantalapiedra-Hijar G, Yáñez-Ruiz DR, Martín- García AI, Molina-Alcaide E (2009) Effects of forage: Concentrate ratio and forage type on apparent digestibility, ruminal fermentation, and microbial growth in oats. Journal of Animal Science 87, 622-631. doi:10.2527/jas.2008-1142
3. Cantalapiedra-Hijar G, Yáñez-Ruiz DR, Newbold CJ, Molina-Alcaide E (2011) The effect of the feed-to-buffer ratio on bacterial diversity and ruminal fermentation in single-flow continuous-culture fermenters. Journal of Dairy Science 87, 622-631
4. Castillejos L, Calsamiglia S, Ferret A, Losa R (2007) Effects of dose and adaptation time of a specific blend of essential oil compounds on rumen fermentation. Animal Feed Science and Technology 132, 186-201. doi:10.1016/j.anifeedsci.2006.03.023
5. Cheng KJ, McAllister TA, Costerton JW (1995) Biofilms of the ruminant digestive tract. In 'Microbial biofilms'. (Eds HM Lappin-Scott, JW Costerton) pp. 221-232. (Cambridge University Press: Cambridge, UK
6. Cho SJ, Cho KM, Shin EC, Lim WJ, Hong SY, Choi BR, Kang JM, Lee SM, Kim YH, Hoon K, Yun HD (2006) 16S rDNA analysis of bacterial diversity in three fractions of cow rumen. Journal of Microbiology and Biotechnology 16, 92-101
7. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18, 117-143. doi:10.1111/j.1442-9993.1993.tb00438.x
8. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM (2009) The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Research 37, D141-D145. doi:10.1093/ nar/gkn879
9. Crawford RJ Jr, HooverWH,KnowltonPH(1980) Effects of solids and liquid flows on fermentation in continuous cultures. I. Dry matter and fiber digestion, VFA production and protozoa numbers. Journal of Animal Science 51, 975-985
10. Czerkawski JW (1969) Methane production in ruminants and its significance. World Review of Nutrition and Dietetics 11, 240-282
11. Denman SE, McSweeney CS (2005) Quantitative (real-time) PCR. In 'Methods in gut microbial ecology for ruminants'. (Eds HPS Makkar, CS McSweeney) pp. 105-115. (Springer: Dordrecht, The Netherlands
12. Denman SE, McSweeney CS (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiology Ecology 58, 572-582.doi:10.1111/j.1574-6941.2006.00190. x
13. Denman SE, Tomkins NW, McSweeney CS (2007) Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiology Ecology 62, 313-322. doi:10.1111/j.1574-6941.2007. 00394.x
14. Engebretson JJ, Moyer CL (2003) Fidelity of select restriction endonucleases in determining microbial diversity by terminalrestriction fragment length polymorphism. Applied and Environmental Microbiology 69(8), 4823-4829. doi:10.1128/AEM.69.8.4823-4829. 2003
15. Gill M, Smith P, Wilkinson JM (2010) Mitigating climate change: The role of domestic livestock. Animal 4, 323-333. doi:10.1017/S17517311090 04662
16. Gizzi G, Zanchi R, Sciaraffia F (1998) Comparison of microbiological and fermentation parameters obtained with an improved rumen in vitro technique with those obtained in vivo. Animal Feed Science and Technology 73, 291-305. doi:10.1016/S0377-8401(98)00150-3
17. Gordon GL, Phillips MW (1989) Degradation and utilization of cellulose and straw by three different anaerobic fungi from the ovine rumen. Applied and Environmental Microbiology 55(7), 1703-1710
18. Hongoh Y, Yuzawa H, Ohkuma M, Kudo T (2003) Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiology Letters 221, 299-304. doi:10.1016/ S0378-1097(03)00218-0
19. Kajikawa H, Jin H, Terada F, Suga T (2003) Operation and characteristics of newly improved and marketable artificial rumen (Rusitec). Memoirs of the National Institute of Livestock and Grassland Science 2, 1-21. [Japan]
20. Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Applied and Environmental Microbiology 69, 6768-6776. doi:10.1128/ AEM.69.11.6768-6776.2003
21. Khafipour E, Li S, Plaizier JC, Krause DO (2009) Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Applied and Environmental Microbiology 75(22), 7115-7124. doi:10.1128/AEM.00739-09
22. Kobayashi Y, Shinkai T, Koike S (2008) Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion - Review. Folia Microbiologica 53, 195-200. doi:10.1007/s12223-008- 0024-z
23. 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 Microbiology Letters 204, 361-366. doi:10.1111/j.1574-6968.2001. tb10911.x
24. Koike S, Yoshitani S, Kobayashi Y, Tanaka K (2003) Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiology Letters 229, 23-30.doi:10.1016/S0378-1097(03)00760-2
25. Kong Y, Teather R, Forster R (2010) Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiology Ecology 74, 612-622. doi:10.1111/j.1574- 6941.2010.00977.x
26. Kruskal JB, WishM (1978) 'Multidimensional scaling.' (Sage Publications: Beverly Hills, CA
27. Latham MJ, Brooker BE, Pettipher GL, Harris PJ (1978) Adhesion of Bacteroides succinogenes in pure culture and in the presence of Ruminococcus flavefaciens to cell walls in leaves of perennial ryegrass (Lolium perenne). Applied and Environmental Microbiology 35, 1166-1173
28. Legendre P, Legendre L (1998) 'Numerical ecology.' 2nd edn. (Elsevier: Amsterdam, The Netherlands
29. Li M, Gong J, Cottrill M, Yu H, de Lange C, Burton J, Topp E (2003) Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota. Journal of Microbiological Methods 54, 13-20.
30. Loesche WJ (1969) Oxygen sensitivity of various anaerobic bacteria. Applied Microbiology 18, 723-727
31. Mackie RI, Gilchrist FMC, Robberts AM, Hannah PE, Schwartz HM (1978) Microbiological and chemical changes in the rumen during the stepwise adaptation of sheep to high concentrate diets. The Journal of Agricultural Science 90(02), 241-254. doi:10.1017/S00218596000 55313
32. Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, Arai H, Tanimoto I, Nishimura F, Takashiba S (2003) Quantitative realtime PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunology and Medical Microbiology 39, 81-86. doi:10.1016/S0928-8244(03)00224-4
33. Mansfield HR, Endres MI, Stern MD (1995) Comparison of microbial fermentation in the rumen of dairy cows and dual flow continuous culture. Animal Feed Science and Technology 55, 47-66. doi:10.1016/ 0377-8401(95)98202-8
34. Martínez ME, Ranilla MJ, Tejido ML, Ramos S, Carro MD (2010a) Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbial growth. Journal of Dairy Science 93(8), 3684-3698. doi:10.3168/jds.2009-2933
35. MartínezME,Ranilla MJ, TejidoML,Saro C, CarroMD(2010b) Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities. Journal of Dairy Science 93(8), 3699-3712. doi:10.3168/jds.2009-2934
36. McDougall EI (1948) Studies on ruminant saliva. 1. The composition and output of sheep's saliva. Biochemical Journal 43, 99-109
37. Michalet-Doreau B, Fernandez I, Peyron C, Millet L, Fonty G (2001) Fibrolytic activities and cellulolytic bacterial community structure in the solid and liquid phases of rumen contents. Reproduction, Nutrition, Development 41, 187-194. doi:10.1051/rnd:2001122
38. Miettinen H, Setälä J (1989) Design and development of a continuous culture system for studying rumen fermentation. Journal of Agricultural Science in Finland 61, 463-473
39. Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 65, 3518-3525
40. Molina-Alcaide E, Pascual MR, Cantalapiedra-Hijar G, Morales- García EY, Martín-García AI (2009) Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters. Journal of Animal Science 87, 1321-1333. doi:10.2527/jas.2008-1263
41. Moumen A, Yáñez-Ruiz DR, Martín-García AI, Molina-Alcaide E (2009) Protozoa evolution in single-flow continuous-culture fermenters and Rusitec fermenters fed high-forage diets. Options Méditerranéenes 85, 303-308
42. Mountfort DO (1987) The rumen anaerobic fungi. FEMS Microbiology Letters 46, 401-408. doi:10.1111/j.1574-6968.1987.tb02476.x
43. Muetzel S, Lawrence P, Hoffmann EM, Becker K (2009) Evaluation of a stratified continuous rumen incubation system. Animal Feed Science and Technology 151, 32-43. doi:10.1016/j.anifeedsci.2008.11.001
44. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59, 695-700
45. Pielou EC (1966) The measurement of diversity in different types of biological collections. Journal of Theoretical Biology 13, 131-144. doi:10.1016/0022-5193(66)90013-0
46. Prevot S, Senaud J, Bohatier J, PrensierG(1994) Variation in the composition of the ruminal bacterial microflora during the adaptation phase in an artificial fermentor (Rusitec). Zoological Science 11, 871-878
47. Prieto C, Aguilera JF, Lara L, Fonollá J (1990) Protein and energy requirements for maintenance of indigenous Granadina goats. The British Journal of Nutrition 63, 155-163. doi:10.1079/BJN19900103
48. Sadet S, Martin C, Meunier B, Morgavi DP (2007) PCR-DGGE analysis reveals a distinct diversity in the bacterial population attached to the rumen epithelium. Animal 1, 939-944. doi:10.1017/S1751731107000304
49. Sadet-Bourgeteau S, Martin C, Morgavi DP (2010) Bacterial diversity dynamics in rumen epithelium of wethers fed forage and mixed concentrate forage diets. Veterinary Microbiology 146, 98-104. doi:10.1016/j.vetmic.2010.04.029
50. Shannon CE, Weaver W (1949) 'The mathematical theory of information.' (University of Illinois Press: Urbana, IL)
51. Shinkai T, Kobayashi Y (2007) Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR. Applied and Environmental Microbiology 73, 1646-1652. doi:10.1128/AEM.01896-06
52. Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ (2007) MiCA: A web-based tool for the analysis of microbial communities based on terminalrestriction fragment length polymorphisms of 16S and 18S rRNA genes. Microbial Ecology 53, 562-570. doi:10.1007/s00248-006-9106-0
53. SørensenT(1948)Amethod of establishing groups of equal amplitude in plant sociology based on similarity of species content and its application to analyses of the vegetation on Danish Commons. Biologiske Skrifter 5, 1-34.
54. Van den Abbeele P, Grootaert C, Marzorati M, Possemiers S, Verstraete W, Gerard P, Rabot S, Bruneau A, El Aidy S, Zoetendal E, Kleerebezem M, Smidt H, Van de Wiele T (2010) Microbial community development in a dynamic gut model is reproducible, colon-region specific and selects for Bacteroidetes and Clostridium Cluster IX. Applied and Environmental Microbiology 76, 5237-5246. doi:10.1128/AEM.00759-10
55. Van Soest PJ, Robertson JB, LewisB(1991) Methods for dietary fiber, neutral detergent fiber, and non-starch polysaccharides in relation to animal nutrition. Journal of Dairy Science 74, 3583-3597. doi:10.3168/jds. S0022-0302(91)78551-2
56. Wiener N (1948) 'Cybernetics or communication and control in the animal and the machine.' (John Wiley and Sons: New York
57. Williams AG (1986) Rumen holotrich ciliate protozoa. Microbiology and Molecular Biology Reviews 50, 25-49.
58. Yu Z, Yu M, Morrison M (2006) Improved serial analysis of V1 ribosomal sequence tags (SARST V1) provides a rapid, comprehensive, sequence based characterization of bacterial diversity and community composition. Environmental Microbiology 8, 603-611. doi:10.1111/j.1462-2920. 2005.00933.x
59. Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA (2000) Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes. Environmental Microbiology 2, 632-643. doi:10.1046/j.1462-2920.2000.00146.x 822 Animal Production Science E. C.