S. D. Allison and J. B. Martiny, Resistance, resilience, and redundancy in microbial communities, Proc. Natl. Acad. Sci. U. S. A, vol.105, pp.11512-11519, 2008.

M. Blanch, S. Calsamiglia, N. Dilorenzo, A. Dicostanzo, S. Muetzel et al., Physiological changes in rumen fermentation during acidosis induction and its control using a multivalent polyclonal antibody preparation in heifers, J. Anim. Sci, vol.87, pp.1722-1730, 2009.

M. M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of, 1976.

, Entodinium above 100 ?m, and (D) Isotricha counts on the last day of the corn silagebased (squares) and hay-based diets (circles) from 6 cows fed 3 experimental periods (EP) of a corn silage-based diet followed by a hay-based diet (EP × diet P-value = 0.026 and 0.035, respectively, for total protozoal and Entodinium below 100 ?m counts and <0.01 and <0.001, respectively, for Entodinium above 100 ?m and Isotricha counts). Bars = cow SD. a-c Counts that do not have a common superscript differ, Anal. Biochem, vol.72, pp.248-254

F. Dohme, T. J. Devries, and K. A. Beauchemin, Repeated ruminal acidosis challenges in lactating dairy cows at high and low risk for developing acidosis: Ruminal pH, J. Dairy Sci, vol.91, pp.3554-3567, 2008.

J. E. Edwards, S. A. Huws, E. J. Kim, and A. H. Kingston-smith, Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen, FEMS Microbiol. Ecol, vol.62, pp.323-335, 2007.

G. J. Faichney, Transit des digesta dans le tube digestif des ruminants. Pages 431-464 in Nutrition des ruminants domestiques. Ingestion et digestion, 1995.

G. Fonty, J. P. Jouany, E. Forano, P. Gouet-;-r.-jarrige, Y. Ruckebusch et al., L'écosystème microbien du réticulo-rumen. Pages 299-348 in Nutrition des ruminants domestiques. Ingestion et digestion, J. Off. République Fr, pp.5608-5610, 1988.

D. W. Goad, C. L. Goad, and T. G. Nagaraja, Ruminal microbial and fermentative changes associated with experimentally induced subacute acidosis in steers, J. Anim. Sci, vol.79, pp.234-241, 1998.

. Ibm, SPSS Statistics 20 Core System, User's Guide, 2011.

M. Ivan, L. Neill, R. Forster, R. Alimon, L. M. Rode et al., Effects of Isotricha, Dasytricha, Entodinium, and total fauna on ruminal fermentation and duodenal fl ow in wethers fed different diets, J. Dairy Sci, vol.83, pp.776-787, 2000.

R. Jarrige, Ruminant Nutrition: Recommended Allowances and Feed Tables, John Libbey, 1989.

C. Julien, J. P. Marden, C. Bonnefont, R. Moncoulon, E. Auclair et al., Effects of varying proportions of concentrates on ruminal reducing power and bacterial community structure in dry dairy cows fed hay-based diets, Animal, vol.4, pp.1641-1646, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02668680

M. D. Krom, Spectrophotometric determination of ammonia, The Analyst, vol.105, pp.305-316, 1980.

J. Marden, C. Bayourthe, F. Enjalbert, and R. Moncoulon, A new device for measuring kinetics of ruminal pH and redox potential in dairy cattle, J. Dairy Sci, vol.88, pp.277-281, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02675548

C. Martin, B. Michalet-doreau, G. Fonty, and A. Williams, Postprandial variations in the activity of polysaccharide-degrading enzymes of fl uid-and particle-associated ruminal microbial populations, Curr. Microbiol, vol.27, pp.223-228, 1993.

R. J. Michelland, S. Dejean, S. Combes, L. Fortun-lamothe, and L. Cauquil, StatFingerprints: A friendly graphical interface program for processing and analysis of microbial fi ngerprint profi les, Mol. Ecol. Res, vol.9, pp.1359-1363, 2009.

R. Michelland, V. Monteils, S. Combes, L. Cauquil, T. Gidenne et al., Changes over time in the bacterial communities associated with fl uid and food particles and the ruminal parameters in the bovine rumen before and after a dietary change, Can. J. Microbiol, vol.57, pp.629-637, 2011.

R. Michelland, V. Monteils, A. Zened, S. Combes, L. Cauquil et al., Spatial and temporal variations of the bacterial community in the bovine digestive tract, J. Appl. Microbiol, vol.107, pp.1642-1650, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02655667

V. Monteils, M. Rey, L. Cauquil, A. Troegeler-meynadier, M. Silberberg et al., Random changes in the heifer rumen in bacterial community structure, physico-chemical and fermentation parameters, and in vitro fi bre degradation. Livestock Sci, vol.141, pp.104-112, 2011.

V. Monteils, M. Rey, and T. Gidenne, Mid to long term stability of ruminal physicochemistry in dairy cows fed a fi bre-or a starch-based diet. Pages 284-285 in XIth Int, Geochim. Cosmochim. Acta, vol.41, pp.1835-1841, 1977.

M. J. Playne, Determination of ethanol, volatile fatty acids, lactic acid and succinic acid in fermentation liquids by gas chromatography, J. Sci. Food Agric, vol.36, pp.638-644, 1985.

F. Privé, S. Combes, L. Cauquil, Y. Farizon, F. Enjalbert et al., Temperature and duration of heating of sunfl ower oil affect ruminal biohydrogenation of linoleic acid in vitro, J. Dairy Sci, vol.93, pp.711-722, 2010.

R. Development-core and . Team, R: A Language and Environment for Statistical Computing. R Found, Stat. Comput, 2009.

A. Ramette, Multivariate analyses in microbial ecology, FEMS Microbiol. Ecol, vol.62, pp.142-160, 2007.

M. J. Ranilla, J. P. Jouany, and D. P. Morgavi, Methane production and substrate degradation by rumen microbial communities containing single protozoal species in vitro, Lett. Appl. Microbiol, vol.45, pp.675-680, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02656278

M. L. Rosenzweig, Species Diversity in Space and Time, 1995.

J. B. Rowe, A. Davies, and A. W. Broome, Quantitative effects of defaunation on rumen fermentation and digestion in sheep, Br. J. Nutr, vol.54, pp.105-119, 1985.

K. Tajima, S. Arai, K. Ogata, T. Nagamine, H. Matsui et al., Rumen bacterial community transition during adaptation to high-grain diet, Anaerobe, vol.6, pp.273-284, 2000.

K. Tajima, T. Nagamine, H. Matsui, M. Nakamura, and R. I. Ami, Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens, FEMS Microbiol. Lett, vol.200, pp.67-72, 2001.

A. G. Williams and G. S. Coleman, The Rumen Protozoa, 1992.