Skip to main content Accessibility help

Cow responses and evolution of the rumen bacterial and methanogen community following a complete rumen content transfer

  • T. De Mulder (a1), L. Vandaele (a1), N. Peiren (a1), A. Haegeman (a2), T. Ruttink (a2), S. De Campeneere (a1), T. Van De Wiele (a3) and K. Goossens (a1)...


Understanding the rumen microbial ecosystem requires the identification of factors that influence the community structure, such as nutrition, physiological condition of the host and host–microbiome interactions. The objective of the current study was to describe the rumen microbial communities before, during and after a complete rumen content transfer. The rumen contents of one donor cow were removed completely and used as inoculum for the emptied rumen of the donor itself and three acceptor cows under identical physiological and nutritional conditions. Temporal changes in microbiome composition and rumen function were analysed for each of four cows over a period of 6 weeks. Shortly after transfer, the cows showed different responses to perturbation of their rumen content. Feed intake depression in the first 2 weeks after transfer resulted in short-term changes in milk production, methane emission, fatty acid composition and rumen bacterial community composition. These effects were more pronounced in two cows, whose microbiome composition showed reduced diversity. The fermentation metrics and microbiome diversity of the other two cows were not affected. Their rumen bacterial community initially resembled the composition of the donor but evolved to a new community profile that resembled neither the donor nor their original composition. Descriptive data presented in the current paper show that the rumen bacterial community composition can quickly recover from a reduction in microbiome diversity after a severe perturbation. In contrast to the bacteria, methanogenic communities were more stable over time and unaffected by stress or host effects.


Corresponding author

Author for correspondence: K. Goossens, E-mail:


Hide All
AlZahal, O, Li, F, Guan, LL, Walker, ND and McBride, BW (2017) Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. Journal of Dairy Science 100, 43774393.
Belanche, A, Doreau, M, Edwards, JE, Moorby, JM, Pinloche, E and Newbold, CJ (2012) Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. Journal of Nutrition 142, 16841692.
Castro-Montoya, J, Peiren, N, Cone, JW, Zweifel, B, Fievez, V and De Campeneere, S (2015) In vivo and in vitro effects of a blend of essential oils on rumen methane mitigation. Livestock Science 180, 134142.
De Boever, JL, Goossens, K, Peiren, N, Swanckaert, J, Ampe, B, Reheul, D, De Brabander, DL, De Campeneere, S and Vandaele, L (2017) The effect of maize silage type on the performances and methane emission of dairy cattle. Journal of Animal Physiology and Animal Nutrition 101, e246e256.
De Campeneere, S and Peiren, N (2014) ILVO's ruminant respiration facility. In Pinares, C and Waghorn, G (eds), Technical Manual on Respiration Chamber Design. Wellington, New Zealand: Ministry of Agriculture and Forestry, pp. 4358.
De Mulder, T, Goossens, K, Peiren, N, Vandaele, L, Haegeman, A, De Tender, C, Ruttink, T, Van de Wiele, T and De Campeneere, S (2017) Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural. FEMS Microbiology Ecology 93, article no. fiw251, 112. doi: 10.1093/femsec/fiw251.
Getachew, G, Makkar, HPS and Becker, K (2001) Method of polyethylene glycol application to tannin-containing browses to improve microbial fermentation and efficiency of microbial protein synthesis from tannin-containing browses. Animal Feed Science and Technology 92, 5157.
Gokarn, RR, Eiteman, MA, Martin, SA and Eriksson, KEL (1997) Production of succinate from glucose, cellobiose, and various cellulosic materials by the ruminal anaerobic bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens. Applied Biochemistry and Biotechnology 68, 6980.
Henderson, G, Cox, F, Ganesh, S, Jonker, A, Young, W, Global Rumen Census Collaborators and Janssen, PH (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports 5, Article No. 14567, 113.
Hook, SE, Northwood, KS, Wright, ADG and McBride, BW (2009) Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Applied and Environmental Microbiology 75, 374380.
Koskella, B and Meaden, S (2013) Understanding bacteriophage specificity in natural microbial communities. Viruses 5, 806823.
Madsen, J, Bjerg, B, Hvelplund, T, Weisbjerg, M and Lund, P (2010) Methane and carbon dioxide ratio in excreted air for quantification of the methane production from ruminants. Livestock Science 129, 223227.
McMurdie, PJ and Holmes, S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217,
Morita, H, Shiratori, C, Murakami, M, Takami, H, Toh, H, Kato, Y, Nakajima, F, Takagi, M, Akita, H, Masaoka, T and Hattori, M (2008) Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses. International Journal of Systematic and Evolutionary Microbiology 58, 26822686.
Nagaraja, TG and Taylor, MB (1987) Susceptibility and resistance of ruminal bacteria to antimicrobial feed additives. Applied and Environmental Microbiology 53, 16201625.
Oksanen, J, Blanchet, FG, Kindt, R, Legendre, P, Minchin, PR, O'Hara, RB, Simpson, GL, Solymos, P, Stevens, MHH and Wagner, H (2015). Package ‘Vegan’: Community Ecology Package. R package version 2.3-2. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from
Ovreas, L, Forney, L, Daae, F and Torsvik, V (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Applied and Environmental Microbiology 63, 33673373.
Prabhu, R, Altman, E and Eiteman, MA (2012) Lactate and acrylate metabolism by Megasphaera elsdenii under batch and steady-state conditions. Applied and Environmental Microbiology 78, 85648570.
Roehe, R, Dewhurst, RJ, Duthie, CA, Rooke, JA, McKain, N, Ross, DW, Hyslop, JJ, Waterhouse, A, Freeman, TC, Watson, M and Wallace, RJ (2016) Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance. PLoS Genetics 12, e1005846,
Russell, JR and Hino, T (1985) Regulation of lactate production in Streptococcus bovis: a spiraling effect that contributes to rumen acidosis. Journal of Dairy Science 68, 17121721.
Shi, WB, Moon, CD, Leahy, SC, Kang, DW, Froula, J, Kittelmann, S, Fan, C, Deutsch, S, Gagic, D, Seedorf, H, Kelly, WJ, Atua, R, Sang, C, Soni, P, Li, D, Pinares-Patino, CS, McEwan, JC, Janssen, PH, Chen, F, Visel, A, Wang, Z, Attwood, GT and Rubin, EM (2014) Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Research 24, 15171525.
Tajima, K, Aminov, RI, Nagamine, T, Matsui, H, Nakamura, M and Benno, Y (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Applied and Environmental Microbiology 67, 27662774.
Tamminga, S, Van Straalen, WM, Subnel, APJ, Meijer, RGM, Steg, A, Wever, CJG and Blok, MC (1994) The Dutch protein evaluation system – the Dve/Oeb-system. Livestock Production Science 40, 139155.
Varel, VH and Jung, HJ (1986) Influence of forage phenolics on ruminal fibrolytic bacteria and in vitro fiber degradation. Applied and Environmental Microbiology 52, 275280.
Vilchez-Vargas, R, Geffers, R, Suárez-Diez, M, Conte, I, Waliczek, A, Kaser, VS, Kralova, M, Junca, H and Pieper, DH (2013) Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environmental Microbiology 15, 10161039.
Vlaming, JB, Lopez-Villalobos, N, Brookes, IM, Hoskin, SO and Clark, H (2008) Within- and between-animal variance in methane emissions in non-lactating dairy cows. Australian Journal of Experimental Agriculture 48, 124127.
Weimer, PJ, Stevenson, DM, Mantovani, HC and Man, SLC (2010) Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents. Journal of Dairy Science 93, 59025912.
Winter, C, Bouvier, T, Weinbauer, MG and Thingstad, TF (2010) Trade-offs between competition and defense specialists among unicellular planktonic organisms: the ‘killing the winner’ hypothesis revisited. Microbiology and Molecular Biology Reviews: MMBR 74, 4257.
Woodward, SL, Waghorn, GC, Ulyatt, MJ and Lassey, KR (2001) Early indications that feeding Lotus will reduce methane emissions from ruminants. Proceedings of the New Zealand Society of Animal Production 61, 2326.
Yu, Z and Morrison, M (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 36, 808812.


Type Description Title
Supplementary materials

De Mulder et al. supplementary material
Figures S1-S2

 Word (609 KB)
609 KB

Cow responses and evolution of the rumen bacterial and methanogen community following a complete rumen content transfer

  • T. De Mulder (a1), L. Vandaele (a1), N. Peiren (a1), A. Haegeman (a2), T. Ruttink (a2), S. De Campeneere (a1), T. Van De Wiele (a3) and K. Goossens (a1)...


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed