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Understanding the Diversity and Roles of the Ruminal Microbiome

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Abstract

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60–85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40–50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

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References

  • Abubakr, A. R., Alimon, A. R., Yaakub, H., Abdullah, N., & 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, 147–154.

    Article  Google Scholar 

  • Akin, D., & Borneman, W. (1990). Role of rumen fungi in fiber degradation. Journal of Dairy Science, 73, 3023–3032.

    Article  CAS  PubMed  Google Scholar 

  • Amin, N., & Seifert, J. (2021). Dynamic progression of the calf’s microbiome and its influence on host health. Computational and Structural Biotechnology Journal, 19, 989–1001.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson, C. L., Sullivan, M. B., & Fernando, S. C. (2017). Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome, 5, 155.

    Article  PubMed  PubMed Central  Google Scholar 

  • Arshad, M. A., Hassan, F. U., Rehman, M. S., Huws, S. A., Cheng, Y., & Din, A. U. (2021). Gut microbiome colonization and development in neonatal ruminants: Strategies, prospects, and opportunities. Animal Nutrition, 7, 883–895.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J. M., et al. (2011). Enterotypes of the human gut microbiome. Nature, 473, 174–180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bauchop, T., & Mountfort, D. O. (1981). Cellulose fermentation by a rumen anaerobic fungus in both the absence and the presence of rumen methanogens. Applied and Environmental Microbiology, 42, 1103–1110.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belanche, A., de la Fuente, G., & Newbold, C. J. (2014). Study of methanogen communities associated with different rumen protozoal populations. FEMS Microbiology Ecology, 90, 663–677.

    Article  CAS  PubMed  Google Scholar 

  • Benson, A. K., Kelly, S. A., Legge, R., Ma, F., Low, S. J., Kim, J., Zhang, M., Oh, P. L., Nehrenberg, D., Hua, K., et al. (2010). Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proceedings of the National Academy of Sciences of the USA, 107, 18933–18938.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bi, Y., Cox, M. S., Zhang, F., Suen, G., Zhang, N., Tu, Y., & Diao, Q. (2019). Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs. Environmental Microbiology, 21, 2333–2346.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bowen, J. M., Cormican, P., Lister, S. J., McCabe, M. S., Duthie, C. A., Roehe, R., & Dewhurst, R. J. (2020). Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation. PLoS One, 15, e0231759.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown, D. (2018). Optimising rumen health and the effect this will have on ketosis. Livestock, 23, 174–178.

    Article  Google Scholar 

  • Brulc, J. M., Antonopoulos, D. A., Miller, M. E., Wilson, M. K., Yannarell, A. C., Dinsdale, E. A., Edwards, R. E., Frank, E. D., Emerson, J. B., Wacklin, P., et al. (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 USA, 106, 1948–1953.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buan, N. R. (2018). Methanogens: Pushing the boundaries of biology. Emerging Topics in Life Sciences, 2, 629–646.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Callaway, T. R., Dowd, S. E., Edrington, T. S., Anderson, R. C., Krueger, N., Bauer, N., Kononoff, P. J., & Nisbet, D. J. (2010). Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. Journal of Animal Science, 88, 3977–3983.

    Article  CAS  PubMed  Google Scholar 

  • Carberry, C. A., Kenny, D. A., Han, S., McCabe, M. S., & Waters, S. M. (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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Castillo-González, A. R., Burrola-Barraza, M. E., Domínguez-Viveros, J., & Chávez-Martínez, A. (2014). Rumen microorganisms and fermentation. Archivos De Medicina Veterinaria, 46, 349–361.

    Article  Google Scholar 

  • Celi, P., Cowieson, A. J., Fru-Nji, F., Steinert, R. E., Kluenter, A. M., & Verlhac, V. (2017). Gastrointestinal functionality in animal nutrition and health: New opportunities for sustainable animal production. Animal Feed Science and Technology, 234, 88–100.

    Article  Google Scholar 

  • Chaucheyras-Durand, F., Ameilbonne, A., Bichat, A., Mosoni, P., Ossa, F., & Forano, E. (2016). Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi. Journal of Applied Microbiology, 120, 560–570.

    Article  CAS  PubMed  Google Scholar 

  • Chaucheyras-Durand, F., & Ossa, F. (2014). REVIEW: The rumen microbiome: Composition, abundance, diversity, and new investigative tools. The Professional Animal Scientist, 30, 1–12.

    Article  Google Scholar 

  • Chen, H., Wang, C., Huasai, S., & Chen, A. (2021). Effects of dietary forage to concentrate ratio on nutrient digestibility, ruminal fermentation and rumen bacterial composition in Angus cows. Scientific Reports, 11, 17023.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clemmons, B. A., Voy, B. H., & Myer, P. R. (2019). Altering the gut microbiome of cattle: Considerations of host-microbiome interactions for persistent microbiome manipulation. Microbial Ecology, 77, 523–536.

    Article  CAS  PubMed  Google Scholar 

  • Cunningham, H. C., Austin, K. J., & Cammack, K. M. (2018a). Influence of maternal factors on the rumen microbiome and subsequent host performance. Translational Animal Science, 2, S101–S105.

    Article  PubMed  PubMed Central  Google Scholar 

  • Cunningham, H. C., Austin, K. J., Powell, S. R., Carpenter, K. T., & Cammack, K. M. (2018b). Potential response of the rumen microbiome to mode of delivery from birth through weaning. Translational Animal Science, 2, S35–S38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Mulder, T., Peiren, N., Vandaele, L., Ruttink, T., De Campeneere, S., Van de Wiele, T., & Goossens, K. (2018). Impact of breed on the rumen microbial community composition and methane emission of Holstein Friesian and Belgian Blue heifers. Livestock Science, 207, 38–44.

    Article  Google Scholar 

  • de Oliveira, M. N., Jewell, K. A., Freitas, F. S., Benjamin, L. A., Tótola, M. R., Borges, A. C., Moraes, C. A., & Suen, G. (2013). Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Veterinary Microbiology, 164, 307–314.

    Article  PubMed  Google Scholar 

  • Delgado, B., Bach, A., Guasch, I., González, C., Elcoso, G., Pryce, J. E., & Gonzalez-Recio, O. (2019). Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle. Scientific Reports, 9, 11.

    Article  PubMed  PubMed Central  Google Scholar 

  • Diao, Q., Zhang, R., & Fu, T. (2019). Review of strategies to promote rumen development in calves. Animals, 9, 490.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dias, J., Marcondes, M. I., Motta de Souza, S., Cardoso da Mata, E. S. B., Fontes Noronha, M., Tassinari Resende, R., Machado, F. S., Cuquetto Mantovani, H., Dill-McFarland, K. A., & Suen, G. (2018). Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development. Applied and Environmental Microbiology, 84, e02675-e2717.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dill-McFarland, K. A., Breaker, J. D., & Suen, G. (2017). Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Scientific Reports, 7, 40864.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du, Y., Gao, Y., Hu, M., Hou, J., Yang, L., Wang, X., Du, W., Liu, J., & Xu, Q. (2023). Colonization and development of the gut microbiome in calves. Journal of Animal Science and Biotechnology, 14, 46.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dušková, D., & Marounek, M. (2001). Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rumen bacterium Lachnospira multiparus. Letters in Applied Microbiology, 33, 159–163.

    Article  PubMed  Google Scholar 

  • Elderman, M., Hugenholtz, F., Belzer, C., Boekschoten, M., van Beek, A., de Haan, B., Savelkoul, H., de Vos, P., & Faas, M. (2018). Sex and strain dependent differences in mucosal immunology and microbiota composition in mice. Biology of Sex Differences, 9, 26.

    Article  PubMed  PubMed Central  Google Scholar 

  • Fenchel, T., & Finlay, B. J. (2006). The diversity of microbes: Resurgence of the phenotype. Philosophical Transactions of the Royal Society B: Biological Sciences, 361, 1965–1973.

    Article  Google Scholar 

  • Fernando, S. C., Purvis, H. T., 2nd., Najar, F. Z., Sukharnikov, L. O., Krehbiel, C. R., Nagaraja, T. G., Roe, B. A., & Desilva, U. (2010). Rumen microbial population dynamics during adaptation to a high-grain diet. Applied and Environmental Microbiology, 76, 7482–7490.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Furman, O., Shenhav, L., Sasson, G., Kokou, F., Honig, H., Jacoby, S., Hertz, T., Cordero, O. X., Halperin, E., & Mizrahi, I. (2020). Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics. Nature Communications, 11, 1904.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia-Vallvé, S., Romeu, A., & Palau, J. (2000). Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Molecular Biology and Evolution, 17, 352–361.

    Article  PubMed  Google Scholar 

  • Gilbert, R. A., Townsend, E. M., Crew, K. S., Hitch, T. C. A., Friedersdorff, J. C. A., Creevey, C. J., Pope, P. B., Ouwerkerk, D., & Jameson, E. (2020). Rumen virus populations: Technological advances enhancing current understanding. Frontiers in Microbiology, 11, 450.

    Article  PubMed  PubMed Central  Google Scholar 

  • Guan, L. L., Nkrumah, J. D., Basarab, J. A., & Moore, S. S. (2008). Linkage of microbial ecology to phenotype: Correlation of rumen microbial ecology to cattle’s feed efficiency. FEMS Microbiology Letters, 288, 85–91.

    Article  CAS  PubMed  Google Scholar 

  • Gutierrez, J., & Davis, R. E. (1962). Culture and metabolism of the rumen ciliate epidinium ecaudatum crawley. Applied Microbiology, 10, 305–308.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guzman, C. E., Bereza-Malcolm, L. T., De Groef, B., & Franks, A. E. (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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Han, X. P., Liu, H. J., Hu, L. Y., Ma, L., Xu, S. X., Xu, T. W., Zhao, N., Wang, X. G., & Chen, Y. W. (2020). Impact of sex and age on the bacterial composition in rumen of Tibetan sheep in Qinghai China. Livestock Science, 238, 104030.

    Article  Google Scholar 

  • He, Y., Wang, H. B., Yu, Z. T., Niu, W. J., Qiu, Q. H., Su, H. W., & Cao, B. H. (2018). Effects of the gender differences in cattle rumen fermentation on anaerobic fermentation of wheat straw. Journal of Cleaner Production, 205, 845–853.

    Article  CAS  Google Scholar 

  • Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Collaborators, G. R. C., & Janssen, P. H. (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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henderson, G., Cox, F., Kittelmann, S., Miri, V. H., Zethof, M., Noel, S. J., Waghorn, G. C., & Janssen, P. H. (2013). Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One, 8, e74787.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hook, S. E., Wright, A. D., & McBride, B. W. (2010). Methanogens: Methane producers of the rumen and mitigation strategies. Archaea, 2010, 945785.

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang, Y., Li, Y., He, B., Hu, J., Ali Mohsin, M., Yu, H., Wang, P., Zhang, P., Du, Y., Huang, L., et al. (2019). The influence of ketosis on the rectal microbiome of Chinese Holstein cows. Pakistan Veterinary Journal, 39, 175–180.

    Article  CAS  Google Scholar 

  • Hungate, R. E. (1975). The rumen microbial ecosystem. Annual Review of Ecology and Systematics, 6, 39–66.

    Article  CAS  Google Scholar 

  • Islam, M., Kim, S. H., Ramos, S. C., Mamuad, L. L., Son, A. R., Yu, Z. T., Lee, S. S., Cho, Y. I., & Lee, S. S. (2021). Holstein and Jersey steers differ in rumen microbiota and enteric methane emissions even fed the same total mixed ration. Frontiers in Microbiology, 12, 601061.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jami, E., Israel, A., Kotser, A., & Mizrahi, I. (2013). Exploring the bovine rumen bacterial community from birth to adulthood. The ISME Journal, 7, 1069–1079.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jami, E., White, B. A., & Mizrahi, I. (2014). Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency. PLoS One, 9, e85423.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jewell, K. A., McCormick, C. A., Odt, C. L., Weimer, P. J., & 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, 4697–4710.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Joblin, K. N. (2005). Methanogenic archaea. In H. P. S. Makkar & C. S. McSweeney (Eds.), Methods in Gut Microbial Ecology for Ruminants (pp. 47–53). Springer. https://doi.org/10.1007/1-4020-3791-0_4

    Chapter  Google Scholar 

  • Johnson, K. A., & Johnson, D. E. (1995). Methane emissions from cattle. Journal of Animal Science, 73, 2483–2492.

    Article  CAS  PubMed  Google Scholar 

  • Khafipour, E., Li, S., Tun, H. M., Derakhshani, H., Moossavi, S., & Plaizier, J. C. (2016). Effects of grain feeding on microbiota in the digestive tract of cattle. Animal Frontiers, 6, 13–19.

    Article  Google Scholar 

  • Kim, M. (2023). Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition. Animal Bioscience, 36, 364–373.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim, Y. H., Nagata, R., Ohkubo, A., Ohtani, N., Kushibiki, S., Ichijo, T., & Sato, S. (2018). Changes in ruminal and reticular pH and bacterial communities in Holstein cattle fed a high-grain diet. BMC Veterinary Research, 14, 310.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kleen, J. L., Hooijer, G. A., Rehage, J., & Noordhuizen, J. P. (2003). Subacute ruminal acidosis (SARA): A review. Journal of Veterinary Medicine Series A, 50, 406–414.

    Article  CAS  PubMed  Google Scholar 

  • Klein-Jobstl, D., Quijada, N. M., Dzieciol, M., Feldbacher, B., Wagner, M., Drillich, M., Schmitz-Esser, S., & Mann, E. (2019). Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves’ gastrointestinal microbiota. PLoS One, 14, e0220554.

    Article  PubMed  PubMed Central  Google Scholar 

  • Klein-Jobstl, D., Schornsteiner, E., Mann, E., Wagner, M., Drillich, M., & Schmitz-Esser, S. (2014). Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Frontiers in Microbiology, 5, 622.

    PubMed  PubMed Central  Google Scholar 

  • Klieve, A. V., O’Leary, M. N., McMillen, L., & Ouwerkerk, D. (2007). Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet. Journal of Applied Microbiology, 103, 2065–2073.

    Article  CAS  PubMed  Google Scholar 

  • Klieve, A. V., Swain, R. A., & Nolan, J. V. (1996). Bacteriophages in the rumen: Types present, population size and implications for the efficiency of feed utilisation. Proceedings of the Australian Society of Animal Production, 21, 92–94.

    Google Scholar 

  • Koike, S., & Kobayashi, Y. (2009). Fibrolytic rumen bacteria: Their ecology and functions. Asian-Australasian Journal of Animal Sciences, 22, 131–138.

    Article  CAS  Google Scholar 

  • Krause, D. O., Denman, S. E., Mackie, R. I., Morrison, M., Rae, A. L., Attwood, G. T., & McSweeney, C. S. (2003). Opportunities to improve fiber degradation in the rumen: Microbiology, ecology, and genomics. FEMS Microbiology Reviews, 27, 663–693.

    Article  CAS  PubMed  Google Scholar 

  • Krause, D., Nagaraja, T., Wright, A., & Callaway, T. (2013). Board-invited review: Rumen microbiology: Leading the way in microbial ecology. Journal of Animal Science, 91, 331–341.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J. H., Kumar, S., Lee, G. H., Chang, D. H., Rhee, M. S., Yoon, M. H., & Kim, B. C. (2013). Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle. International Journal of Systematic and Evolutionary Microbiology, 63, 4196–4201.

    Article  CAS  PubMed  Google Scholar 

  • Lefkowitz, E. J., Dempsey, D. M., Hendrickson, R. C., Orton, R. J., Siddell, S. G., & Smith, D. B. (2018). Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Research, 46, D708–D717.

    Article  CAS  PubMed  Google Scholar 

  • Li, F., & Guan, L. L. (2017). Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle. Applied and Environmental Microbiology, 83, e00061-e117.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, F. Y., Hitch, T. C. A., Chen, Y. H., Creevey, C. J., & Guan, L. L. (2019). Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. Microbiome, 7, 6.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, R. W., Connor, E. E., Li, C., Baldwin Vi, R. L., & Sparks, M. E. (2012). Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environmental Microbiology, 14, 129–139.

    Article  PubMed  Google Scholar 

  • Li, Z. P., Liu, H. L., Li, G. Y., Bao, K., Wang, K. Y., Xu, C., Yang, Y. F., Yang, F. H., & Wright, A. D. (2013). Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China. BMC Microbiology, 13, 151.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, Z. M., Shi, J. P., Lei, Y., Wu, J. P., Zhang, R., Zhang, X., Jia, L., Wang, Y., Ma, Y., He, P. J., et al. (2022). Castration alters the cecal microbiota and inhibits growth in Holstein cattle. Journal of Animal Science, 100, skac367.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lobo, R. R., & Faciola, A. P. (2021). Ruminal phages—a review. Frontiers in Microbiology, 12, 763416.

    Article  PubMed  PubMed Central  Google Scholar 

  • Majak, W., McAllister, T. A., McCartney, D., Stanford, K., & Cheng, J. J. (2003). Bloat in cattle. Alberta Agriculture and Rural Development.

    Google Scholar 

  • Malmuthuge, N., Li, M., Goonewardene, L. A., Oba, M., & Guan, L. L. (2013). Effect of calf starter feeding on gut microbial diversity and expression of genes involved in host immune responses and tight junctions in dairy calves during weaning transition. Journal of Dairy Science, 96, 3189–3200.

    Article  CAS  PubMed  Google Scholar 

  • Martin, S. A. (1994). Nutrient transport by ruminal bacteria: A review. Journal of Animal Science, 72, 3019–3031.

    Article  CAS  PubMed  Google Scholar 

  • Martínez-Álvaro, M., Auffret, M. D., Duthie, C. A., Dewhurst, R. J., Cleveland, M. A., Watson, M., & Roehe, R. (2022). Bovine host genome acts on rumen microbiome function linked to methane emissions. Communications Biology, 5, 350.

    Article  PubMed  PubMed Central  Google Scholar 

  • Martínez-Álvaro, M., Auffret, M. D., Stewart, R. D., Dewhurst, R. J., Duthie, C. A., Rooke, J. A., Wallace, R. J., Shih, B., Freeman, T. C., Watson, M., et al. (2020). Identification of complex rumen microbiome interaction within diverse functional niches as mechanisms affecting the variation of methane emissions in bovine. Frontiers in Microbiology, 11, 659.

    Article  PubMed  PubMed Central  Google Scholar 

  • Matthews, C., Crispie, F., Lewis, E., Reid, M., O’Toole, P. W., & Cotter, P. D. (2019). The rumen microbiome: A crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency. Gut Microbes, 10, 115–132.

    Article  CAS  PubMed  Google Scholar 

  • McCann, J. C., Luan, S., Cardoso, F. C., Derakhshani, H., Khafipour, E., & Loor, J. J. (2016). Induction of subacute ruminal acidosis affects the ruminal microbiome and epithelium. Frontiers in Microbiology, 7, 701.

    Article  PubMed  PubMed Central  Google Scholar 

  • McCann, J. C., Wickersham, T. A., & Loor, J. J. (2014). High-throughput methods redefine the rumen microbiome and its relationship with nutrition and metabolism. Bioinformatics and Biology Insights, 8, 109–125.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McSweeney, C., & Mackie, R. (2012). Micro-organisms and ruminant digestion: State of knowledge, trends and future prospects. Commision on Genetic Resources for Food and Agriculture, Background Study Paper (FAO), 61, 1–62. https://www.fao.org/3/me992e/me992e.pdf.

  • Meale, S. J., Li, S., Azevedo, P., Derakhshani, H., Plaizier, J. C., Khafipour, E., & Steele, M. A. (2016). Development of ruminal and fecal microbiomes are affected by weaning but not weaning strategy in dairy calves. Frontiers in Microbiology, 7, 582.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mebius, R. E. (2003). Organogenesis of lymphoid tissues. Nature Reviews Immunology, 3, 292–303.

    Article  CAS  PubMed  Google Scholar 

  • Mitsumori, M., Xu, L., Kajikawa, H., Kurihara, M., Tajima, K., Hai, J., & Takenaka, A. (2003). Possible quorum sensing in the rumen microbial community: Detection of quorum-sensing signal molecules from rumen bacteria. FEMS Microbiology Letters, 219, 47–52.

    Article  CAS  PubMed  Google Scholar 

  • Mizrahi, I. (2013). Rumen symbioses. In E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, & F. Thompson (Eds.), The Prokaryotes: Prokaryotic biology and symbiotic associations (pp. 533–544). Springer.

    Chapter  Google Scholar 

  • Mizrahi, I., & Jami, E. (2018). Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission. Animal, 12, S220–S232.

    Article  CAS  PubMed  Google Scholar 

  • Moraïs, S., & Mizrahi, I. (2019). Islands in the stream: From individual to communal fiber degradation in the rumen ecosystem. FEMS Microbiology Reviews, 43, 362–379.

    Article  PubMed  PubMed Central  Google Scholar 

  • Morgavi, D. P., Kelly, W. J., Janssen, P. H., & Attwood, G. T. (2013). Rumen microbial (meta)genomics and its application to ruminant production. Animal, 7, 184–201.

    Article  CAS  PubMed  Google Scholar 

  • Mosoni, P., Martin, C., Forano, E., & Morgavi, D. P. (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, 783–791.

    Article  CAS  PubMed  Google Scholar 

  • Mountfort, D. O. (1987). The rumen anaerobic fungi. FEMS Microbiology Reviews, 3, 401–408.

    Article  Google Scholar 

  • Myer, P. R., Smith, T. P., Wells, J. E., Kuehn, L. A., & Freetly, H. C. (2015). Rumen microbiome from steers differing in feed efficiency. PLoS One, 10, e0129174.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nagaraja, T. G. (2016). Microbiology of the Rumen. In D. Millen, M. De Beni Arrigoni, & R. Lauritano Pacheco (Eds.), Rumenology (pp. 39–61). Springer. https://doi.org/10.1007/978-3-319-30533-2_2

    Chapter  Google Scholar 

  • Nagaraja, T. G., & Titgemeyer, E. C. (2007). Ruminal acidosis in beef cattle: The current microbiological and nutritional outlook. Journal of Dairy Science, 90, E17–E38.

    Article  PubMed  Google Scholar 

  • Nathani, N. M., Patel, A. K., Mootapally, C. S., Reddy, B., Shah, S. V., Lunagaria, P. M., Kothari, R. K., & Joshi, C. G. (2015). Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis). BMC Genomics, 16, 1116.

    Article  PubMed  PubMed Central  Google Scholar 

  • Negash, A. (2022). Gut microbiota ecology role in animal nutrition and health performance. Journal of Clinical Microbiology and Antimicrobials, 6, 001.

    Google Scholar 

  • Newbold, C. J., de La Fuente, G., Belanche, A., Ramos-Morales, E., & McEwan, N. R. (2015). The role of ciliate protozoa in the rumen. Frontiers in Microbiology, 6, 1313.

    Article  PubMed  PubMed Central  Google Scholar 

  • Newbold, C. J., & Ramos-Morales, E. (2020). Review: Ruminal microbiome and microbial metabolome: Effects of diet and ruminant host. Animal, 14, s78–s86.

    Article  CAS  PubMed  Google Scholar 

  • Oetzel, G. R. (2003). Subacute ruminal acidosis in dairy cattle. Advances in Dairy Technology, 15, 307–317.

    Google Scholar 

  • Ogata, T., Kim, Y. H., Masaki, T., Iwamoto, E., Ohtani, Y., Orihashi, T., Ichijo, T., & Sato, S. (2019). Effects of an increased concentrate diet on rumen pH and the bacterial community in Japanese Black beef cattle at different fattening stages. The Journal of Veterinary Medical Science, 81, 968–974.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ogunade, I., Pech-Cervantes, A., & Schweickart, H. (2019). Metatranscriptomic analysis of sub-acute ruminal acidosis in beef cattle. Animals, 9, 232.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ozutsumi, Y., Tajima, K., Takenaka, A., & Itabashi, H. (2005). The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries. Bioscience, Biotechnology, and Biochemistry, 69, 499–506.

    Article  CAS  PubMed  Google Scholar 

  • Paul, R., Williams, A., & Butler, R. (1990). Hydrogenosomes in the rumen entodiniomorphid ciliate Polyplastron multivesiculatum. Microbiology, 136, 1981–1989.

    CAS  Google Scholar 

  • Paynter, M. J., & Hungate, R. E. (1968). Characterization of Methanobacterium mobilis, sp. n., isolated from the bovine rumen. Journal of Bacteriology, 95, 1943–1951.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pitta, D. W., Indugu, N., Kumar, S., Vecchiarelli, B., Sinha, R., Baker, L. D., Bhukya, B., & Ferguson, J. D. (2016a). Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows. Anaerobe, 38, 50–60.

    Article  CAS  PubMed  Google Scholar 

  • Pitta, D. W., Pinchak, E., Dowd, S. E., Osterstock, J., Gontcharova, V., Youn, E., Dorton, K., Yoon, I., Min, B. R., Fulford, J. D., et al. (2010). Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets. Microbial Ecology, 59, 511–522.

    Article  PubMed  Google Scholar 

  • Pitta, D. W., Pinchak, W. E., Indugu, N., Vecchiarelli, B., Sinha, R., & Fulford, J. D. (2016b). Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat. Frontiers in Microbiology, 7, 689.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plaizier, J. C., Li, S., Danscher, A. M., Derakshani, H., Andersen, P. H., & Khafipour, E. (2017). Changes in microbiota in rumen digesta and feces due to a grain-based Subacute Ruminal Acidosis (SARA) challenge. Microbial Ecology, 74, 485–495.

    Article  CAS  PubMed  Google Scholar 

  • Ramos, S. C., Jeong, C. D., Mamuad, L. L., Kim, S. H., Kang, S. H., Kim, E. T., Cho, Y. I., Lee, S. S., & Lee, S. S. (2021). Diet transition from high-forage to high-concentrate alters rumen bacterial community composition, epithelial transcriptomes and ruminal fermentation parameters in dairy cows. Animals, 11, 838.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rey, M., Enjalbert, F., Combes, S., Cauquil, L., Bouchez, O., & Monteils, V. (2014). Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential. Journal of Applied Microbiology, 116, 245–257.

    Article  CAS  PubMed  Google Scholar 

  • Rey, M., Enjalbert, F., & Monteils, V. (2012). Establishment of ruminal enzyme activities and fermentation capacity in dairy calves from birth through weaning. Journal of Dairy Science, 95, 1500–1512.

    Article  CAS  PubMed  Google Scholar 

  • Ricard, G., McEwan, N., Dutilh, B., Jouany, J., Macheboeuf, D., Mitsumori, M., McIntosh, F., Michalowski, T., Nagamine, T., Nelson, N., et al. (2006). Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics, 7, 22.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019). What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms, 7, 14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Russell, J. B., & Baldwin, R. L. (1978). Substrate preferences in rumen bacteria: Evidence of catabolite regulatory mechanisms. Applied and Environmental Microbiology, 36, 319–329.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scharen, M., Frahm, J., Kersten, S., Meyer, U., Hummel, J., Breves, G., & Danicke, S. (2018). Interrelations between the rumen microbiota and production, behavioral, rumen fermentation, metabolic, and immunological attributes of dairy cows. Journal of Dairy Science, 101, 4615–4637.

    Article  CAS  PubMed  Google Scholar 

  • Scollan, N., Hocquette, J., Richardson, R., & Kim, E. (2011). Raising the nutritional value of beef and beef products to add value in beef production. In J. D. Wood & C. Rowlings (Eds.), Nutrition and climate change: Major issues confronting the meat industry (pp. 79–104). Nottingham University Press.

    Google Scholar 

  • Seymour, W. M., Campbell, D. R., & Johnson, Z. B. (2005). Relationships between rumen volatile fatty acid concentrations and milk production in dairy cows: A literature study. Animal Feed Science and Technology, 119, 155–169.

    Article  CAS  Google Scholar 

  • Sim, S., Lee, H., Yoon, S., Seon, H., Park, C., & Kim, M. (2022). The impact of different diets and genders on fecal microbiota in Hanwoo cattle. Journal of Animal Science and Technology, 64, 897–910.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sinha, T., Vich Vila, A., Garmaeva, S., Jankipersadsing, S. A., Imhann, F., Collij, V., Bonder, M. J., Jiang, X., Gurry, T., Alm, E. J., et al. (2019). Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes, 10, 358–366.

    Article  CAS  PubMed  Google Scholar 

  • Smith, P. M., & Garrett, W. S. (2011). The gut microbiota and mucosal T cells. Frontiers in Microbiology, 2, 111.

    Article  PubMed  PubMed Central  Google Scholar 

  • Solomon, R., & Jami, E. (2021). Rumen protozoa: From background actors to featured role in microbiome research. Environmental Microbiology Reports, 13, 45–49.

    Article  PubMed  Google Scholar 

  • Solomon, R., Wein, T., Levy, B., Eshed, S., Dror, R., Reiss, V., Zehavi, T., Furman, O., Mizrahi, I., & Jami, E. (2022). Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem. The ISME Journal, 16, 1187–1197.

    Article  PubMed  Google Scholar 

  • Song, Y., Malmuthuge, N., Li, F., & Guan, L. L. (2019). Colostrum feeding shapes the hindgut microbiota of dairy calves during the first 12 h of life. FEMS Microbiology Ecology, 95, fiy203.

    Article  CAS  Google Scholar 

  • Song, Y., Malmuthuge, N., Steele, M. A., & Guan, L. L. (2018). Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. FEMS Microbiology Ecology, 94, fix179.

    Google Scholar 

  • Sprockett, D., Fukami, T., & Relman, D. A. (2018). Role of priority effects in the early-life assembly of the gut microbiota. Nature Reviews Gastroenterology & Hepatology, 15, 197–205.

    Article  Google Scholar 

  • Stevenson, D. M., & Weimer, P. J. (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, 165–174.

    Article  CAS  PubMed  Google Scholar 

  • Stewart, C. S., Duncan, S. H., Richardson, A. J., Backwell, C., & Begbie, R. (1992). The inhibition of fungal cellulolysis by cell-free preparations from ruminococci. FEMS Microbiology Letters, 97, 83–87.

    Article  CAS  Google Scholar 

  • Sylvester, J. T., Karnati, S. K., Yu, Z., Morrison, M., & Firkins, J. L. (2004). Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. The Journal of Nutrition, 134, 3378–3384.

    Article  CAS  PubMed  Google Scholar 

  • Tajima, K., Arai, S., Ogata, K., Nagamine, T., Matsui, H., Nakamura, M., Aminov, R. I., & Benno, Y. (2000). Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe, 6, 273–284.

    Article  CAS  Google Scholar 

  • Tao, N., DePeters, E. J., German, J. B., Grimm, R., & Lebrilla, C. B. (2009). Variations in bovine milk oligosaccharides during early and middle lactation stages analyzed by high-performance liquid chromatography-chip/mass spectrometry. Journal of Dairy Science, 92, 2991–3001.

    Article  CAS  PubMed  Google Scholar 

  • Tapio, I., Snelling, T. J., Strozzi, F., & Wallace, R. J. (2017). The ruminal microbiome associated with methane emissions from ruminant livestock. Journal of Animal Science and Biotechnology, 8, 7.

    Article  PubMed  PubMed Central  Google Scholar 

  • Thauer, R. K., Kaster, A. K., Seedorf, H., Buckel, W., & Hedderich, R. (2008). Methanogenic archaea: Ecologically relevant differences in energy conservation. Nature Reviews Microbiology, 6, 579–591.

    Article  CAS  PubMed  Google Scholar 

  • Turnbaugh, P. J., & Gordon, J. I. (2009). The core gut microbiome, energy balance and obesity. The Journal of Physiology, 587, 4153–4158.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uyeno, Y., Sekiguchi, Y., Tajima, K., Takenaka, A., Kurihara, M., & Kamagata, Y. (2010). An rRNA-based analysis for evaluating the effect of heat stress on the rumen microbial composition of Holstein heifers. Anaerobe, 16, 27–33.

    Article  CAS  PubMed  Google Scholar 

  • van Wolferen, M., Pulschen, A. A., Baum, B., Gribaldo, S., & Albers, S. V. (2022). The cell biology of archaea. Nature Microbiology, 7, 1744–1755.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vlková, E., Trojanová, I., & Rada, V. (2006). Distribution of bifidobacteria in the gastrointestinal tract of calves. Folia Microbiologica, 51, 325–328.

    Article  PubMed  Google Scholar 

  • Wang, L., Li, Y., Zhang, Y., & Wang, L. (2020). The effects of different concentrate-to-forage ratio diets on rumen bacterial microbiota and the structures of Holstein cows during the feeding cycle. Animals, 10, 957.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, L., Wu, D. Y., Zhang, Y., Li, K., Wang, M. J., & Ma, J. P. (2023). Dynamic distribution of gut microbiota in cattle at different breeds and health states. Frontiers in Microbiology, 14, 1113730.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, L., Xu, Q., Kong, F., Yang, Y., Wu, D., Mishra, S., & Li, Y. (2016). Exploring the goat rumen microbiome from seven days to two years. PLoS One, 11, e0154354.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, L., Zhang, K., Zhang, C., Feng, Y., Zhang, X., Wang, X., & Wu, G. (2019). Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep. Scientific Reports, 9, 19620.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, S., Giller, K., Kreuzer, M., Ulbrich, S. E., Braun, U., & Schwarm, A. (2017). Contribution of ruminal fungi, archaea, protozoa, and bacteria to the methane suppression caused by oilseed supplemented diets. Frontiers in Microbiology, 8, 1864.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, Y., Majak, W., & McAllister, T. A. (2012). Frothy bloat in ruminants: Cause, occurrence, and mitigation strategies. Animal Feed Science and Technology, 172, 103–114.

    Article  Google Scholar 

  • Weimer, P. J. (2015). Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations. Frontiers in Microbiology, 6, 296.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wright, A. D. G., & Klieve, A. V. (2011). Does the complexity of the rumen microbial ecology preclude methane mitigation? Animal Feed Science and Technology, 166–167, 248–253.

    Article  Google Scholar 

  • Xu, Q., Qiao, Q., Gao, Y., Hou, J., Hu, M., Du, Y., Zhao, K., & Li, X. (2021). Gut microbiota and their role in health and metabolic disease of dairy cow. Frontiers in Nutrition, 8, 701511.

    Article  PubMed  PubMed Central  Google Scholar 

  • Yarlett, N., Orpin, C., Munn, E., Yarlett, N., & Greenwood, C. (1986). Hydrogenosomes in the rumen fungus Neocallimastix patriciarum. Biochemical Journal, 236, 729–739.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yeoman, C. J., Ishaq, S. L., Bichi, E., Olivo, S. K., Lowe, J., & Aldridge, B. M. (2018). Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract. Scientific Reports, 8, 3197.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zehnder, A. J. B., & Wuhrmann, K. (1977). Physiology of a Methanobacterium strain AZ. Archives of Microbiology, 111, 199–205.

    Article  CAS  Google Scholar 

  • Zeineldin, M., Barakat, R., Elolimy, A., Salem, A. Z., Elghandour, M. M., & Monroy, J. C. (2018). Synergetic action between the rumen microbiota and bovine health. Microbial Pathogenesis, 124, 106–115.

    Article  PubMed  Google Scholar 

  • Zhou, Z., Fang, L., Meng, Q., Li, S., Chai, S., Liu, S., & Schonewille, J. T. (2017). Assessment of ruminal bacterial and archaeal community structure in yak (Bos grunniens). Frontiers in Microbiology, 8, 179.

    PubMed  PubMed Central  Google Scholar 

  • Zhu, Z., Kristensen, L., Difford, G. F., Poulsen, M., Noel, S. J., Abu Al-Soud, W., Sørensen, S. J., Lassen, J., Løvendahl, P., & Højberg, O. (2018). Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows. Journal of Dairy Science, 101, 9847–9862.

    Article  CAS  PubMed  Google Scholar 

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Keum, G.B., Pandey, S., Kim, E.S. et al. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol. 62, 217–230 (2024). https://doi.org/10.1007/s12275-024-00121-4

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