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Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission

  • I. Mizrahi (a1) and E. Jami (a2)


The rumen microbiome has the important task of supplying ruminants with most of their dietary requirements and is responsible for up to 90% of their metabolic needs. This tremendous feat is possible due to the large diversity of microorganisms in the rumen. The rumen is considered one of the most diverse ecosystems on the planet in terms of species diversity and functional richness. From the moment the feed is ingested, it enters a vast cascade in which specialized microorganisms degrade specific components of the feed turning them into molecules, which in turn are utilized as anabolic precursors and energy sources for the animal. The output of this degradation process not only affects the animal, but also has an extensive impact on the environment. Some of the byproducts that are emitted as waste from this process, such as methane, act as greenhouse gases which greatly contribute to global warming. Recent technological advances developed to study this community enabled a larger overview of its vast taxonomic and functional diversity, thus leading to a better understanding of its ecology and function. This deeper understanding of the forces affecting the microbiome includes the forces that shape composition, the variation among animals, the stability of its key components, the processes of succession on a short- and long-time scales such as primary colonization and diurnal oscillations. These collective understandings have helped to provide insights into the potential effects that these forces have on the outputs observed from the animal itself. Over the recent years, there has been a growing body of evidence demonstrating the link between the microbiome and its effect on productivity of the host animals and the environment, which has placed rumen microbiome studies in the forefront of animal agricultural research. In this review, we focus on the natural variations in community composition, which are not the results of different management or feed but rather intrinsic features of animals. We characterize the rumen microbiome, its potential impact on its host as well as the barriers in implementing the current knowledge to modulate the microbiome and point toward potential avenues to overcome these hurdles.

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Abecia, L, Martín-García, AI, Martínez, G, Newbold, CJ and Yáñez-Ruiz, DR 2013. Nutritional intervention in early life to manipulate rumen microbial colonization and methane output by kid goats postweaning. Journal of Animal Science 91, 48324840.
Abecia, L, Waddams, KE, Martínez-Fernandez, G, Martín-García, AI, Ramos-Morales, E, Newbold, CJ and Yáñez-Ruiz, DR 2014. An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by archaea. Archaea 2014, 841463.
Abubakr, AR, Alimon, AR, Yaakub, H, Abdullah, N and Ivan, M 2013. Digestibility, rumen protozoa, and ruminal fermentation in goats receiving dietary palm oil by-products. Journal of the Saudi Society of Agricultural Sciences 12, 147154.
Accetto, T and Avguštin, G 2015. Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species. Systematic and Applied Microbiology 38, 453461.
Akin, DE and Borneman, WS 1990. Role of rumen fungi in fiber degradation. Journal of Dairy Science 73, 30233032.
Artegoitia, VM, Middleton, JL, Harte, FM, Campagna, SR and de Veth, MJ 2014. Choline and choline metabolite patterns and associations in blood and milk during lactation in dairy cows. PloS One 9, e103412.
Attwood, GT, Lockington, RA, Xue, GP and Brooker, JD 1988. Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen. Applied and Environmental Microbiology 54, 534539.
Belanche, A, de la Fuente, G and Newbold, CJ 2014. Study of methanogen communities associated with different rumen protozoal populations. FEMS Microbiology Ecology 90, 663677.
Belanche, A, de la Fuente, G and Newbold, CJ 2015. Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions. FEMS Microbiology Ecology 91, fiu026.
Bergman, EN 1990. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiological Reviews 70, 567590.
Brulc, JM, Antonopoulos, DA, Miller, ME, Wilson, MK, Yannarell, AC, Dinsdale, EA, Edwards, RE, Frank, ED, Emerson, JB, Wacklin, P, Coutinho, PM, Henrissat, B, Nelson, KE and White, BA 2009. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America 106, 19481953.
Carberry CA, Kenny DA, Han S, McCabe MS and Waters SM 2012. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Applied and environmental microbiology 78, 4949–4958.
Carberry, CA, Kenny, DA, Kelly, AK and Waters, SM 2014a. Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets. Journal of Animal Science and Biotechnology 5, 41.
Carberry, CA, Waters, SM, Waters, SM, Kenny, DA and Creevey, CJ 2014b. Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type. Applied and Environmental Microbiology 80, 586594.
Caron, DA, Worden, AZ, Countway, PD, Demir, E and Heidelberg, KB 2009. Protists are microbes too: a perspective. The ISME Journal 3, 412.
Chiquette, J, Allison, MJ and Rasmussen, MA 2008. Prevotella bryantii 25A used as a probiotic in early-lactation dairy cows: effect on ruminal fermentation characteristics, milk production, and milk composition. Journal of Dairy Science 91, 35363543.
Chiquette, J, Talbot, G, Markwell, F, Nili, N and Forster, RJ 2007. Repeated ruminal dosing of Ruminococcus flavefaciens NJ along with a probiotic mixture in forage or concentrate-fed dairy cows: effect on ruminal fermentation, cellulolytic populations and in sacco digestibility. Canadian Journal of Animal Science 87, 237249.
Comtet-Marre, S, Parisot, N, Lepercq, P, Chaucheyras-Durand, F, Mosoni, P, Peyretaillade, E, Bayat, AR, Shingfield, KJ, Peyret, P and Forano, E 2017. Metatranscriptomics reveals the active bacterial and eukaryotic fibrolytic communities in the rumen of dairy cow fed a mixed diet. Frontiers in Microbiology 8, 67.
Costello, EK, Stagaman, K, Dethlefsen, L, Bohannan, BJ and Relman, DA 2012. The application of ecological theory toward an understanding of the human microbiome. Science 336, 12551262.
Danielsson, R, Dicksved, J, Sun, L, Gonda, H, Müller, B, Schnürer, A and Bertilsson, J 2017. Methane production in dairy cows correlates with rumen methanogenic and bacterial community structure. Frontiers in Microbiology 8, 226.
De Filippo, C, Cavalieri, D, Di Paola, M, Ramazzotti, M, Poullet, JB, Massart, S, Collini, S, Pieraccini, G and Lionetti, P 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the United States of America 107, 1469114696.
de Menezes, AB, Lewis, E, O’Donovan, M, O’Neill, BF, Clipson, N and Doyle, EM 2011. Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiology Ecology 78, 256265.
Deusch, S, Camarinha-Silva, A, Conrad, J, Beifuss, U, Rodehutscord, M and Seifert, J 2017. A structural and functional elucidation of the rumen microbiome influenced by various diets and microenvironments. Frontiers in Microbiology 8, 1605.
Diamond, J 1997. Guns, germs, and steel: the fates of human societies. W.W. Norton, New York, NY, USA.
Dill-McFarland, KA, Breaker, JD and Suen, G 2017. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Scientific Reports 7, 40864.
Edwards, JE, Forster, RJ, Callaghan, TM, Dollhofer, V, Dagar, SS, Cheng, Y, Chang, J, Kittelmann, S, Fliegerova, K, Puniya, AK, Henske, JK, Gilmore, SP, O’Malley, MA, Griffith, GW and Smidt, H 2017. PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi: insights, challenges and opportunities. Frontiers in Microbiology 8, 1657.
Flint, HJ, Bisset, J and Webb, J 1989. Use of antibiotic resistance mutations to track strains of obligately anaerobic bacteria introduced into the rumen of sheep. The Journal of Applied Bacteriology 67, 177183.
Fonty, G, Gouet, P, Jouany, J-P and Senaud, J 1987. Establishment of the microflora and anaerobic fungi in the rumen of lambs. Journal of General Microbiology 133, 18351843.
Fonty, G, Jouany, JP, Thivend, P, Gouet, P and Senaud, J 1983. A descriptive study of rumen digestion in meroxenic lambs according to the nature and complexity of the microflora. Reproduction, Nutrition, Development 23, 857873.
Friedman, N, Jami, E and Mizrahi, I 2017. Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages. Environmental Microbiology 8, 33653373.
Friedman, N, Shriker, E, Gold, B, Durman, T, Zarecki, R, Ruppin, E and Mizrahi, I 2016. Diet‐induced changes of redox potential underlie compositional shifts in the rumen archaeal community. Environmental Microbiology 19, 174184.
Guan, LL, Nkrumah, JD, Basarab, JA and Moore, SS 2008. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle’s feed efficiency. FEMS Microbiology Letters 288, 8591.
Guzman, CE, Bereza-Malcolm, LT, De Groef, B and Franks, AE 2015. Presence of selected methanogens, fibrolytic bacteria, and proteobacteria in the gastrointestinal tract of neonatal dairy calves from birth to 72 hours. PloS One 10, e0133048.
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, 14567.
Henderson, G, Cox, F, Kittelmann, S, Miri, VH, Zethof, M, Noel, SJ, Waghorn, GC and Janssen, PH 2013. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PloS One 8, e74787.
Hernandez-Sanabria, E, Guan, LL, Goonewardene, LA, Li, M, Mujibi, DF, Stothard, P, Moore, SS and Leon-Quintero, MC 2010. Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits. Applied and Environmental Microbiology 76, 63386350.
Hess, M, Sczyrba, A, Egan, R, Kim, T-W, Chokhawala, H, Schroth, G, Luo, S, Clark, DS, Chen, F, Zhang, T, Mackie, RI, Pennacchio, LA, Tringe, SG, Visel, A, Woyke, T, Wang, Z and Rubin, EM 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463467.
Hill, KJ and Mangan, JL 1964. The formation and distribution of methylamine in the ruminant digestive tract. Biochemical Journal 93, 3945.
Iino, T, Tamaki, H, Tamazawa, S, Ueno, Y, Ohkuma, M, Suzuki, K-I, Igarashi, Y and Haruta, S 2013. Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes and Environments/ 28, 244250.
Indugu, N, Vecchiarelli, B, Baker, LD, Ferguson, JD, Vanamala, JKP and Pitta, DW 2017. Comparison of rumen bacterial communities in dairy herds of different production. BMC Microbiology 17, 190.
Ishaq, SL, AlZahal, O, Walker, N and McBride, B 2017. An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation. Frontiers in Microbiology 8, 1943.
Jami, E, Israel, A, Kotser, A and Mizrahi, I 2013. Exploring the bovine rumen bacterial community from birth to adulthood. The ISME Journal 7, 10691079.
Jami, E and Mizrahi, I 2012a. Composition and similarity of bovine rumen microbiota across individual animals. PloS One 7, e33306.
Jami, E and Mizrahi, I 2012b. Similarity of the ruminal bacteria across individual lactating cows. Anaerobe 18, 338343.
Jami, E, White, BA and Mizrahi, I 2014. Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency. PloS One 9, e85423.
Jewell, KA, McCormick, CA, Odt, CL, Weimer, PJ and Suen, G 2015. Ruminal bacterial community composition in dairy cows is dynamic over the course of two lactations and correlates with feed efficiency. Applied and Environmental Microbiology 81, 46974710.
Johnson, DE and Ward, GM 1996. Estimates of animal methane emissions. Environmental Monitoring and Assessment 42, 133141.
Kamke, J, Kittelmann, S, Soni, P, Li, Y, Tavendale, M, Ganesh, S, Janssen, PH, Shi, W, Froula, J and Rubin, EM 2016. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4, 56.
Kay, R 1969. Digestion of protein in the intestines of adult ruminants. The Proceedings of the Nutrition Society 28, 140151.
Kim, M, Morrison, M and Yu, Z 2011. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiology Ecology 76, 4963.
Kobayashi, Y, Yamada, M and Yamamoto, M 2001. Survival of a recombinant rumen bacterium in the rumen of sheep. Nihon Chikusan Gakkaiho 72, 344346.
Koetschan, C, Kittelmann, S, Lu, J, Al-Halbouni, D, Jarvis, GN, Müller, T, Wolf, M and Janssen, PH 2014. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PloS One 9, e91928.
Korabecna, M 2007. The variability in the fungal ribosomal DNA (ITS1, ITS2, and 5.8 S rRNA gene): its biological meaning and application in medical mycology. Communicating Current Research and Educational Topics and Trends in Applied Microbiology 2, 783787.
Krause, DO, Bunch, RJ, Conlan, LL, Kennedy, PM, Smith, WJ, Mackie, RI and McSweeney, CS 2001a. Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes. Microbiology 147, 17191729.
Krause, DO, Bunch, RJ, Dalrymple, BD, Gobius, KS, Smith, WJ, Xue, GP and McSweeney, CS 2001b. Expression of a modified Neocallimastix patriciarum xylanase in Butyrivibrio fibrisolvens digests more fibre but cannot effectively compete with highly fibrolytic bacteria in the rumen. Journal of Applied Microbiology 90, 388396.
Krause, DO, Smith, WJ, Ryan, FM, Mackie, RI and McSweeney, CS 1999. Use of 16S-rRNA based techniques to investigate the ecological succession of microbial populations in the immature lamb rumen: tracking of a specific strain of inoculated ruminococcus and interactions with other microbial populations in vivo. Microbial Ecology 38, 365376.
Krishnamoorthy, U and Moran, J 2012. Rearing young ruminants on milk replacers and starter feeds. FAO Animal Production and Health, Rome, Italy.
Kristensen, NB, Bryrup, T, Allin, KH, Nielsen, T, Hansen, TH and Pedersen, O 2016. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Medicine 8, 52.
Kumar, S, Indugu, N, Vecchiarelli, B and Pitta, DW 2015. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows. Frontiers in Microbiology 6, 781.
Lambie, SC, Kelly, WJ, Leahy, SC, Li, D, Reilly, K, McAllister, TA, Valle, ER, Attwood, GT and Altermann, E 2015. The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1. Standards in Genomic Sciences 10, 57.
Layeghifard, M, Hwang, DM and Guttman, DS 2017. Disentangling interactions in the microbiome: a network perspective. Trends in Microbiology 25, 217228.
Ley, RE 2016. Gut microbiota in 2015: prevotella in the gut: choose carefully. Nature Reviews. Gastroenterology & Hepatology 13, 6970.
Li, F and Guan, LL 2017. Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle. Applied and Environmental Microbiology 75, 6524–6533.
Li, RW, Connor, EE, Li, C, Baldwin Vi, RL and Sparks, ME 2012. Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environmental Microbiology 14, 129139.
Li, M, Penner, GB, Hernandez-Sanabria, E, Oba, M and Guan, LL 2009. Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen. Journal of Applied Microbiology 107, 19241934.
Li, Z, Wright, A-DG, Si, H, Wang, X, Qian, W, Zhang, Z and Li, G 2016. Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses. Environmental Microbiology Reports 8, 10161023.
Liggenstoffer, AS, Youssef, NH, Couger, MB and Elshahed, MS 2010. Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. The ISME Journal 4, 12251235.
Lysons, RJ, Alexander, TJ, Wellstead, PD, Hobson, PN, Mann, SO and Stewart, CS 1976. Defined bacterial populations in the rumens of gnotobiotic lambs. Journal of General Microbiology 94, 257269.
Maldonado-Gómez, MX, Martínez, I, Bottacini, F, O’Callaghan, A, Ventura, M, van Sinderen, D, Hillmann, B, Vangay, P, Knights, D, Hutkins, RW and Walter, J 2016. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host & Microbe 20, 515526.
Mann, SO and Stewart, CS 1974. Establishment of a limited rumen flora in gnotobiotic lambs fed on a roughage diet. Journal of General Microbiology 84, 379382.
McCann, JC, Wiley, LM, Forbes, TD, Rouquette, FM Jr and Tedeschi, LO 2014. Relationship between the rumen microbiome and residual feed intake-efficiency of Brahman bulls stocked on bermudagrass pastures. PloS One 9, e91864.
Minato, H, Otsuka, M, Shirasaka, S, Itabashi, H and Mitsumori, M 1992. Colonization of microorganisms in the rumen of young calves. The Journal of General and Applied Microbiology 38, 447456.
Miyagi, T, Kaneichi, K, Aminov, RI, Kobayashi, Y, Sakka, K, Hoshino, S and Ohmiya, K 1995. Enumeration of transconjugated Ruminococcus albus and its survival in the goat rumen microcosm. Applied and Environmental Microbiology 61, 20302032.
Mizrahi, I 2013. Rumen symbioses. In The prokaryotes (ed. E Rosenberg, EF DeLong, S Lory, E Stackebrandt and F Thompson), pp. 533544. Springer, Berlin/Heidelberg.
Monard C, Gantner S and Stenlid J 2013. Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing. FEMS microbiology ecology 84, 165–175.
Morgavi, DP, Forano, E, Martin, C and Newbold, CJ 2010. Microbial ecosystem and methanogenesis in ruminants. Animal 4, 10241036.
Mosoni, P, Martin, C, Forano, E and Morgavi, DP 2011. Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep. Journal of Animal Science 89, 783791.
Neill, AR, Grime, DW and Dawson, RM 1978. Conversion of choline methyl groups through trimethylamine into methane in the rumen. Biochemical Journal 170, 529535.
Newbold, CJ, de la Fuente, G, Belanche, A, Ramos-Morales, E and McEwan, NR 2015. The role of ciliate protozoa in the rumen. Frontiers in Microbiology 6, 1313.
Nkamga, VD and Drancourt, M 2016. Methanomassiliicoccaceae. In Bergey’s manual of systematics of Archaea and Bacteria (ed. WB Whitman). John Wiley & Sons Ltd, Chichester, UK. doi:10.1002/9781118960608.fbm00269.
O’Herrin, SM and Kenealy, WR 1993. Glucose and carbon dioxide metabolism by Succinivibrio dextrinosolvens . Applied and Environmental Microbiology 59, 748755.
Oren, A and Garrity, GM 2015. List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 65, 37633767.
Patra, A, Park, T, Kim, M and Yu, Z 2017. Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances. Journal of Animal Science and Biotechnology 8, 13.
Paul, K, Nonoh, JO, Mikulski, L and Brune, A 2012. ‘Methanoplasmatales,’ thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Applied and Environmental Microbiology 78, 82458253.
Pope, PB, Smith, W, Denman, SE, Tringe, SG, Barry, K, Hugenholtz, P, McSweeney, CS, McHardy, AC and Morrison, M 2011. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333, 646648.
Poulsen, M, Schwab, C, Jensen, BB, Engberg, RM, Spang, A, Canibe, N, Højberg, O, Milinovich, G, Fragner, L and Schleper, C 2013. Methylotrophic methanogenic thermoplasmata implicated in reduced methane emissions from bovine rumen. Nature Communications 4, 1428.
Præsteng, KE, Pope, PB, Cann, IKO, Mackie, RI, Mathiesen, SD, Folkow, LP, Eijsink, VGH and Sundset, MA 2013. Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer. Microbial Ecology 66, 840849.
Rey, M, Enjalbert, F, Combes, S, Cauquil, L, Bouchez, O and Monteils, V 2013. Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential. Journal of Applied Microbiology 116, 245257.
Ribeiro, GO, Oss, DB, He, Z, Gruninger, RJ, Elekwachi, C, Forster, RJ, Yang, W, Beauchemin, KA and McAllister, TA 2017. Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle. Scientific Reports 7, 1276.
Roehe, R, Dewhurst, RJ, Duthie, C-A, 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.
Sander, EG, Warner, RG, Harrison, HN and Loosli, JK 1959. The stimulatory effect of sodium butyrate and sodium propionate on the development of rumen mucosa in the young calf. Journal of Dairy Science 42, 16001605.
Sasson, G, Kruger Ben-Shabat, S, Seroussi, E, Doron-Faigenboim, A, Shterzer, N, Yaacoby, S, Berg Miller, ME, White, BA, Halperin, E and Mizrahi, I 2017. Heritable bovine rumen bacteria are phylogenetically related and correlated with the cow’s capacity to harvest energy from its feed. mBio 8, e00703e00717.
Shabat, SKB, Sasson, G, Doron-Faigenboim, A, Durman, T, Yaacoby, S, Miller, MEB, White, BA, Shterzer, N and Mizrahi, I 2016. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. The ISME Journal 10, 29582972.
Shade, A and Handelsman, J 2012. Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology 14, 412.
Shi, W, Moon, CD, Leahy, SC, Kang, D, Froula, J, Kittelmann, S, Fan, C, Deutsch, S, Gagic, D and Seedorf, H 2014. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Research 24, 15171525.
Skillman, LC, Evans, PN, Naylor, GE, Morvan, B, Jarvis, GN and Joblin, KN 2004. 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe 10, 277285.
Stevenson, DM and Weimer, PJ 2007. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Applied Microbiology and Biotechnology 75, 165174.
Sylvester, JT, Karnati, SKR, Yu, Z, Morrison, M and Firkins, JL 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. The Journal of Nutrition 134, 33783384.
Tapio, I, Fischer, D, Blasco, L, Tapio, M, Wallace, RJ, Bayat, AR, Ventto, L, Kahala, M, Negussie, E, Shingfield, KJ and Vilkki, J 2017a. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PloS One 12, e0180260.
Tapio, I, Snelling, TJ, Strozzi, F and Wallace, RJ 2017b. The ruminal microbiome associated with methane emissions from ruminant livestock. Journal of Animal Science and Biotechnology 8, 7.
Taxis, TM, Wolff, S, Gregg, SJ, Minton, NO, Zhang, C, Dai, J, Schnabel, RD, Taylor, JF, Kerley, MS, Pires, JC, Lamberson, WR and Conant, GC 2015. The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Research 43, 96009612.
Thauer, RK, Kaster, A-K, Seedorf, H, Buckel, W and Hedderich, R 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews. Microbiology 6, 579591.
Turnbaugh, PJ, Ley, RE, Mahowald, MA, Magrini, V, Mardis, ER and Gordon, JI 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 10271031.
Ungerfeld, EM 2013. A theoretical comparison between two ruminal electron sinks. Frontiers in Microbiology 4, 319.
Ungerfeld, EM 2015. Shifts in metabolic hydrogen sinks in the methanogenesis-inhibited ruminal fermentation: a meta-analysis. Frontiers in Microbiology 6, 37.
Vaidya, JD, van den Bogert, B, Edwards, JE, Boekhorst, J, van Gastelen, S, Saccenti, E, Plugge, CM and Smidt, H 2018. The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows. Frontiers in Microbiology 9, 92.
van Lingen, HJ, Plugge, CM, Fadel, JG, Kebreab, E, Bannink, A and Dijkstra, J 2016. Thermodynamic driving force of hydrogen on rumen microbial metabolism: a theoretical investigation. PloS One 11, e0161362.
Van Soest, PJ 1994. Nutritional ecology of the ruminant. Cornell University Press, New York, NY, USA.
Wallace, RJ 1979. Effect of ammonia concentration on the composition, hydrolytic activity and nitrogen metabolism of the microbial flora of the rumen. The Journal of Applied Bacteriology 47, 443455.
Wallace, RJ, Rooke, JA, McKain, N, Duthie, C-A, Hyslop, JJ, Ross, DW, Waterhouse, A, Watson, M and Roehe, R 2015. The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 16, 839.
Wallace, RJ, Snelling, TJ, McCartney, CA, Tapio, I and Strozzi, F 2017. Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genetics, Selection, Evolution 49, 9.
Wallace, RJ and Walker, ND 1993. Isolation and attempted introduction of sugar alcohol-utilizing bacteria in the sheep rumen. The Journal of Applied Bacteriology 74, 353359.
Weimer, PJ 2015. Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations. Frontiers in Microbiology 6, 296.
Weimer, PJ, Cabral, LDS and Cacite, F 2015. Effects of ruminal dosing of Holstein cows with Megasphaera elsdenii on milk fat production, ruminal chemistry, and bacterial strain persistence. Journal of Dairy Science 98, 80788092.
Weimer, PJ, Cox, MS, de Paula, TV, Lin, M, Hall, MB and Suen, G 2017. Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high-and low-efficiency Holstein cows. Journal of Dairy Science 100, 71657182.
Weimer, PJ, Stevenson, DM, Mantovani, HC and Man, S 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.
Welkie, DG, Stevenson, DM and Weimer, PJ 2009. ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle. Anaerobe 16, 94100.
Williams, AG and Coleman, GS 2012. The rumen protozoa. Springer-Verlag, New York, NY, USA.
Yáñez-Ruiz, DR, Williams, S and Newbold, CJ 2007. The effect of absence of protozoa on rumen biohydrogenation and the fatty acid composition of lamb muscle. The British Journal of Nutrition 97, 938948.
Yatsunenko, T, Rey, FE, Manary, MJ, Trehan, I, Dominguez-Bello, MG, Contreras, M, Magris, M, Hidalgo, G, Baldassano, RN, Anokhin, AP, Heath, AC, Warner, B, Reeder, J, Kuczynski, J, Caporaso, JG, Lozupone, CA, Lauber, C, Clemente, JC, Knights, D, Knight, R and Gordon, JI 2012. Human gut microbiome viewed across age and geography. Nature 486, 222227.
Zebeli, Q, Terrill, SJ, Mazzolari, A, Dunn, SM, Yang, WZ and Ametaj, BN 2012. Intraruminal administration of Megasphaera elsdenii modulated rumen fermentation profile in mid-lactation dairy cows. The Journal of Dairy Research 79, 1625.
Zeisel, SH, Mar, M-H, Howe, JC and Holden, JM 2003. Concentrations of choline-containing compounds and betaine in common foods. The Journal of Nutrition 133, 13021307.
Zhou, MI, Hernandez-Sanabria, E and Guan LL 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Applied and Environmental Microbiology 75, 65246533.
Zhou, M, Hernandez-Sanabria, E and Guan, LL 2010. Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis. Applied and Environmental Microbiology 76, 37763786.
Zhou, M, Peng, Y-J, Chen, Y, Klinger, CM, Oba, M, Liu, J-X and Guan, LL 2018. Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle. Microbiome 6, 62.


Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission

  • I. Mizrahi (a1) and E. Jami (a2)


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