<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.3 20210610//EN" "JATS-journalpublishing1-3.dtd">
<article article-type="review-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">meat</journal-id><journal-title-group><journal-title xml:lang="en">Theory and practice of meat processing</journal-title><trans-title-group xml:lang="ru"><trans-title>Теория и практика переработки мяса</trans-title></trans-title-group></journal-title-group><issn pub-type="ppub">2414-438X</issn><issn pub-type="epub">2414-441X</issn><publisher><publisher-name>ФГБНУ «Федеральный научный центр пищевых систем им. В.М. Горбатова» РАН</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.21323/2414-438X-2026-11-1-45-56</article-id><article-id custom-type="elpub" pub-id-type="custom">meat-552</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>Статьи</subject></subj-group></article-categories><title-group><article-title>The rumen microbiome: Abrief review</article-title><trans-title-group xml:lang="ru"><trans-title>The rumen microbiome: Abrief review</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-5969-2054</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Novikova</surname><given-names>А. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Novikova</surname><given-names>A. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Alina A. Novikova, Master of Science in Biomedical Sciences, Assistant, Head of the Laboratory of Systems and Product Quality Control, Department of Bioeconomics and Biosafety, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><bio xml:lang="en"><p>Alina A. Novikova, Master of Science in Biomedical Sciences, Assistant, Head of the Laboratory of Systems and Product Quality Control, Department of Bioeconomics and Biosafety, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><email xlink:type="simple">novikova.aaleksand@dvfu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-3665-1484</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Maksimenko</surname><given-names>А. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Maksimenko</surname><given-names>A. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Anastasiia A. Maksimenko, PhD in Agriculture, Associate Professor, Department of Integrated Projects, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School</p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><bio xml:lang="en"><p>Anastasiia A. Maksimenko, PhD in Agriculture, Associate Professor, Department of Integrated Projects, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School</p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><email xlink:type="simple">maksimenko.aal@dvfu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0002-1692-9802</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Sidorenko</surname><given-names>A. V.</given-names></name><name name-style="western" xml:lang="en"><surname>Sidorenko</surname><given-names>A. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Andrey V. Sidorenko, Assistant Professor, Department of Integrated Projects, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><bio xml:lang="en"><p>Andrey V. Sidorenko, Assistant Professor, Department of Integrated Projects, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><email xlink:type="simple">sidorenko.avla@dvfu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-7450-4362</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Podvolotskaya</surname><given-names>A. B.</given-names></name><name name-style="western" xml:lang="en"><surname>Podvolotskaya</surname><given-names>A. B.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Anna B. Podvolotskaya, Candidate of Medical Sciences, Dean of the Faculty of Bioeconomics and Biosafety, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><bio xml:lang="en"><p>Anna B. Podvolotskaya, Candidate of Medical Sciences, Dean of the Faculty of Bioeconomics and Biosafety, Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><email xlink:type="simple">podvolotckaia.ab@dvfu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-0498-3764</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Tekutyeva</surname><given-names>L. A.</given-names></name><name name-style="western" xml:lang="en"><surname>Tekutyeva</surname><given-names>L. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Liudmila A. Tekutyeva, Candidate of Technical Sciences, Institute of Biotechnology, Bioengineering and Food Systems, Director of Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><bio xml:lang="en"><p>Liudmila A. Tekutyeva, Candidate of Technical Sciences, Institute of Biotechnology, Bioengineering and Food Systems, Director of Advanced Engineering School </p><p>10 Ajax Bay, Russky Island, 690922, Vladivostok</p></bio><email xlink:type="simple">tekuteva.la@dvfu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Far Eastern Federal University<country>Россия</country></aff><aff xml:lang="en">Far Eastern Federal University<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2026</year></pub-date><pub-date pub-type="epub"><day>04</day><month>04</month><year>2026</year></pub-date><volume>11</volume><issue>1</issue><fpage>45</fpage><lpage>56</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Novikova A.A., Maksimenko A.A., Sidorenko A.V., Podvolotskaya A.B., Tekutyeva L.A., 2026</copyright-statement><copyright-year>2026</copyright-year><copyright-holder xml:lang="ru">Novikova А.А., Maksimenko А.В., Sidorenko A.V., Podvolotskaya A.B., Tekutyeva L.A.</copyright-holder><copyright-holder xml:lang="en">Novikova A.A., Maksimenko A.A., Sidorenko A.V., Podvolotskaya A.B., Tekutyeva L.A.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://www.meatjournal.ru/jour/article/view/552">https://www.meatjournal.ru/jour/article/view/552</self-uri><abstract><p>The rumen microbiome is a complex dynamic community of microorganisms that participate in digestion and provide an utmost impact on the cattle efficiency. Despite significant advancements in microbiome research, understanding the formation and management of the rumen microbiome still remains a significant scientific challenge. This topic holds both economic and environmental importance. The purpose of this literature review is to analyze and arrange structurally the current knowledge about the composition and functions of the rumen microbiome for further application of this knowledge in livestock farming. The article emphasizes that diet is an important factor that defines the composition and variability of the microbiome. This work demonstrates that the main functions of the rumen are provided by mutually coordinated groups of bacteria, methanogenic archaea, bacteriophages, protozoa, and fungi. The review covers various microbial groups in the rumen and their functions, as well as the factors that influence changes in the microbial community. Traditional methods of studying the rumen microbiome, based on culture-based techniques, have been significantly improved by the introduction of modern sequencing technologies. The review also explores the history of microbiome research and the “Hungate 1000 collection” project. This work demonstrates how metagenomics, metatranscriptomics, and metaproteomics have not only discovered numerous previously unknown microorganisms, but also provided insights into their functional roles. The systematization of knowledge presented in this review provides a comprehensive understanding of the rumen microbiome as a dynamic object for innovation targeted at improving the productivity, sustainability, and environmental safety of modern livestock farming. </p></abstract><trans-abstract xml:lang="ru"><p>The rumen microbiome is a complex dynamic community of microorganisms that participate in digestion and provide an utmost impact on the cattle efficiency. Despite significant advancements in microbiome research, understanding the formation and management of the rumen microbiome still remains a significant scientific challenge. This topic holds both economic and environmental importance. The purpose of this literature review is to analyze and arrange structurally the current knowledge about the composition and functions of the rumen microbiome for further application of this knowledge in livestock farming. The article emphasizes that diet is an important factor that defines the composition and variability of the microbiome. This work demonstrates that the main functions of the rumen are provided by mutually coordinated groups of bacteria, methanogenic archaea, bacteriophages, protozoa, and fungi. The review covers various microbial groups in the rumen and their functions, as well as the factors that influence changes in the microbial community. Traditional methods of studying the rumen microbiome, based on culture-based techniques, have been significantly improved by the introduction of modern sequencing technologies. The review also explores the history of microbiome research and the “Hungate 1000 collection” project. This work demonstrates how metagenomics, metatranscriptomics, and metaproteomics have not only discovered numerous previously unknown microorganisms, but also provided insights into their functional roles. The systematization of knowledge presented in this review provides a comprehensive understanding of the rumen microbiome as a dynamic object for innovation targeted at improving the productivity, sustainability, and environmental safety of modern livestock farming.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>rumen</kwd><kwd>rumen microbiology</kwd><kwd>microbiome</kwd><kwd>anaerobic bacteria</kwd><kwd>fungi</kwd></kwd-group><kwd-group xml:lang="en"><kwd>rumen</kwd><kwd>rumen microbiology</kwd><kwd>microbiome</kwd><kwd>anaerobic bacteria</kwd><kwd>fungi</kwd></kwd-group><funding-group xml:lang="ru"><funding-statement>This work was supported by the Ministry of Education and Science of the Russian Federation (Agreement on the provision of grants from the federal budget in the form of subsidies in accordance with paragraph 4 of Article 78.1 of the Budget Code of the Russian Federation No. 075-15-2022-1143 dated July 7, 2022).</funding-statement></funding-group><funding-group xml:lang="en"><funding-statement>This work was supported by the Ministry of Education and Science of the Russian Federation (Agreement on the provision of grants from the federal budget in the form of subsidies in accordance with paragraph 4 of Article 78.1 of the Budget Code of the Russian Federation No. 075-15-2022-1143 dated July 7, 2022).</funding-statement></funding-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Abecia, L. et al. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports, 5(1), Article 14567. https://doi.org/10.1038/srep14567</mixed-citation><mixed-citation xml:lang="en">Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Abecia, L. et al. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports, 5(1), Article 14567. https://doi.org/10.1038/srep14567</mixed-citation></citation-alternatives></ref><ref id="cit2"><label>2</label><citation-alternatives><mixed-citation xml:lang="ru">Mao, Y., Wang, F., Kong, W., Wang, R., Liu, X., Ding, H. et al. (2023). Dynamic changes of rumen bacteria and their fermentative ability in high-producing dairy cows during the late perinatal period. Frontiers in Microbiology, 14, Article 1269123. https://doi.org/10.3389/fmicb.2023.1269123</mixed-citation><mixed-citation xml:lang="en">Mao, Y., Wang, F., Kong, W., Wang, R., Liu, X., Ding, H. et al. (2023). Dynamic changes of rumen bacteria and their fermentative ability in high-producing dairy cows during the late perinatal period. Frontiers in Microbiology, 14, Article 1269123. https://doi.org/10.3389/fmicb.2023.1269123</mixed-citation></citation-alternatives></ref><ref id="cit3"><label>3</label><citation-alternatives><mixed-citation xml:lang="ru">Solomon, R., Wein, T., Levy, B., Eshed, S., Dror, R., Reiss, V. et al. (2022). Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem. The ISME Journal, 16(4), 1187– 1197. https://doi.org/10.1038/s41396-021-01170-y</mixed-citation><mixed-citation xml:lang="en">Solomon, R., Wein, T., Levy, B., Eshed, S., Dror, R., Reiss, V. et al. (2022). Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem. The ISME Journal, 16(4), 1187– 1197. https://doi.org/10.1038/s41396-021-01170-y</mixed-citation></citation-alternatives></ref><ref id="cit4"><label>4</label><citation-alternatives><mixed-citation xml:lang="ru">Wang, R., He, S., Huang, D., He, S., Guo, T., Chen, T. et al. (2023). Differences in composition and diversity of rumen fungi in buff lo fed different diets. Animal Biotechnology, 34(9), 5075–5086. https://doi.org/10.1080/10495398.2023.2276974</mixed-citation><mixed-citation xml:lang="en">Wang, R., He, S., Huang, D., He, S., Guo, T., Chen, T. et al. (2023). Differences in composition and diversity of rumen fungi in buff lo fed different diets. Animal Biotechnology, 34(9), 5075–5086. https://doi.org/10.1080/10495398.2023.2276974</mixed-citation></citation-alternatives></ref><ref id="cit5"><label>5</label><citation-alternatives><mixed-citation xml:lang="ru">Wang, H., Li, P., Liu, X., Zhang, C., Lu, Q., Xi, D. et al. (2019). The composition of fungal communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow cattle (Bos taurs). Polish Journal of Microbiology, 68(4), 505–514. https://doi.org/10.33073/pjm-2019-050</mixed-citation><mixed-citation xml:lang="en">Wang, H., Li, P., Liu, X., Zhang, C., Lu, Q., Xi, D. et al. (2019). The composition of fungal communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow cattle (Bos taurs). Polish Journal of Microbiology, 68(4), 505–514. https://doi.org/10.33073/pjm-2019-050</mixed-citation></citation-alternatives></ref><ref id="cit6"><label>6</label><citation-alternatives><mixed-citation xml:lang="ru">Anderson, C. J., Koester, L. R., Schmitz-Esser, S. (2021). Rumen epithelial communities share a core bacterial microbiota: A meta-analysis of 16S rRNA Gene Illumina MiSeq sequencing datasets. Frontiers in Microbiology, 12, Article 625400. https://doi.org/10.3389/fmicb.2021.625400</mixed-citation><mixed-citation xml:lang="en">Anderson, C. J., Koester, L. R., Schmitz-Esser, S. (2021). Rumen epithelial communities share a core bacterial microbiota: A meta-analysis of 16S rRNA Gene Illumina MiSeq sequencing datasets. Frontiers in Microbiology, 12, Article 625400. https://doi.org/10.3389/fmicb.2021.625400</mixed-citation></citation-alternatives></ref><ref id="cit7"><label>7</label><citation-alternatives><mixed-citation xml:lang="ru">Weimer, P. J.(2015). Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations. Frontiers in Microbiology, 6, Article 296. https://doi.org/10.3389/fmicb.2015.00296</mixed-citation><mixed-citation xml:lang="en">Weimer, P. J.(2015). Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations. Frontiers in Microbiology, 6, Article 296. https://doi.org/10.3389/fmicb.2015.00296</mixed-citation></citation-alternatives></ref><ref id="cit8"><label>8</label><citation-alternatives><mixed-citation xml:lang="ru">Krehbiel, C. R. (2014). Invited review: Applied nutrition of ruminants: Fermentation and digestive physiology. The Professional Animal Scientist, 30(2), 129–139. https://doi.org/10.15232/S1080-7446(15)30100-5</mixed-citation><mixed-citation xml:lang="en">Krehbiel, C. R. (2014). Invited review: Applied nutrition of ruminants: Fermentation and digestive physiology. The Professional Animal Scientist, 30(2), 129–139. https://doi.org/10.15232/S1080-7446(15)30100-5</mixed-citation></citation-alternatives></ref><ref id="cit9"><label>9</label><citation-alternatives><mixed-citation xml:lang="ru">Sbardellati, D. L., Fischer, A., Cox, M. S., Li, W., Kalscheur, K. F., Suen, G. (2020). The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of Dairy Science, 103(4), 3636– 3647. https://doi.org/10.3168/jds.2019-17649</mixed-citation><mixed-citation xml:lang="en">Sbardellati, D. L., Fischer, A., Cox, M. S., Li, W., Kalscheur, K. F., Suen, G. (2020). The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of Dairy Science, 103(4), 3636– 3647. https://doi.org/10.3168/jds.2019-17649</mixed-citation></citation-alternatives></ref><ref id="cit10"><label>10</label><citation-alternatives><mixed-citation xml:lang="ru">Ma, Z., Wang, R., Wang, M., Zhang, X., Mao, H., Tan, Z. (2018). Short communication: Variability in fermentation end-products and methanogen communities in different rumen sites of dairy cows. Journal of Dairy Science, 101(6), 5153–5158. https://doi.org/10.3168/jds.2017-14096</mixed-citation><mixed-citation xml:lang="en">Ma, Z., Wang, R., Wang, M., Zhang, X., Mao, H., Tan, Z. (2018). Short communication: Variability in fermentation end-products and methanogen communities in different rumen sites of dairy cows. Journal of Dairy Science, 101(6), 5153–5158. https://doi.org/10.3168/jds.2017-14096</mixed-citation></citation-alternatives></ref><ref id="cit11"><label>11</label><citation-alternatives><mixed-citation xml:lang="ru">Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M. et al. (2018). Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future. Frontiers in Microbiology, 9, Article 2161. https://doi.org/10.3389/fmicb.2018.02161</mixed-citation><mixed-citation xml:lang="en">Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M. et al. (2018). Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future. Frontiers in Microbiology, 9, Article 2161. https://doi.org/10.3389/fmicb.2018.02161</mixed-citation></citation-alternatives></ref><ref id="cit12"><label>12</label><citation-alternatives><mixed-citation xml:lang="ru">Lobo, R. R., Faciola, A. P. (2021). Ruminal phages — A review. Frontiers in Microbiology, 12, Article 763416. https://doi.org/10.3389/fmicb.2021.763416</mixed-citation><mixed-citation xml:lang="en">Lobo, R. R., Faciola, A. P. (2021). Ruminal phages — A review. Frontiers in Microbiology, 12, Article 763416. https://doi.org/10.3389/fmicb.2021.763416</mixed-citation></citation-alternatives></ref><ref id="cit13"><label>13</label><citation-alternatives><mixed-citation xml:lang="ru">Qi, W., Xue, M.-Y., Jia, M.-H., Zhang, S., Yan, Q., Sun, H.-Z. (2024). Understanding the functionality of the rumen microbiota: Searching for better opportunities for rumen microbial manipulation. Animal Bioscience, 37(2), 370–384. https://doi.org/10.5713/ab.23.0308</mixed-citation><mixed-citation xml:lang="en">Qi, W., Xue, M.-Y., Jia, M.-H., Zhang, S., Yan, Q., Sun, H.-Z. (2024). Understanding the functionality of the rumen microbiota: Searching for better opportunities for rumen microbial manipulation. Animal Bioscience, 37(2), 370–384. https://doi.org/10.5713/ab.23.0308</mixed-citation></citation-alternatives></ref><ref id="cit14"><label>14</label><citation-alternatives><mixed-citation xml:lang="ru">Jiang, B., Qin, C., Xu, Y., Song, X., Fu, Y., Li, R. et al. (2024). Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes. Frontiers in Microbiology, 15, Article 1301292. https://doi.org/10.3389/fmicb.2024.1301292</mixed-citation><mixed-citation xml:lang="en">Jiang, B., Qin, C., Xu, Y., Song, X., Fu, Y., Li, R. et al. (2024). Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes. Frontiers in Microbiology, 15, Article 1301292. https://doi.org/10.3389/fmicb.2024.1301292</mixed-citation></citation-alternatives></ref><ref id="cit15"><label>15</label><citation-alternatives><mixed-citation xml:lang="ru">Wu, R., Ji, P., Hua, Y., Li, H., Zhang, W., Wei, Y. (2024). Research progress in isolation and identification of rumen probiotics. Frontiers in Cellular and Infection Microbiology, 14, Article 1411482. https://doi.org/10.3389/fcimb.2024.1411482</mixed-citation><mixed-citation xml:lang="en">Wu, R., Ji, P., Hua, Y., Li, H., Zhang, W., Wei, Y. (2024). Research progress in isolation and identification of rumen probiotics. Frontiers in Cellular and Infection Microbiology, 14, Article 1411482. https://doi.org/10.3389/fcimb.2024.1411482</mixed-citation></citation-alternatives></ref><ref id="cit16"><label>16</label><citation-alternatives><mixed-citation xml:lang="ru">Friedersdorff, J.C. A., Thomas, B. J., Pidcock, S. E., Hart, E. H., Rubino, F., Creevey, C. J.(2020). Genome sequencing and the rumen microbiome. Chapter in a book: Improving rumen function. Burleigh Dodds Science Publishing, 2020. https://doi.org/10.19103/AS.2020.0067.06</mixed-citation><mixed-citation xml:lang="en">Friedersdorff, J.C. A., Thomas, B. J., Pidcock, S. E., Hart, E. H., Rubino, F., Creevey, C. J.(2020). Genome sequencing and the rumen microbiome. Chapter in a book: Improving rumen function. Burleigh Dodds Science Publishing, 2020. https://doi.org/10.19103/AS.2020.0067.06</mixed-citation></citation-alternatives></ref><ref id="cit17"><label>17</label><citation-alternatives><mixed-citation xml:lang="ru">Monroe, C. F., Perkins, A. E. (1939). A study of the pH values of the ingesta of the bovine rumen. Journal of Dairy Science, 22(12), 983–991. https://doi.org/10.3168/jds.S00220302(39)92951-6</mixed-citation><mixed-citation xml:lang="en">Monroe, C. F., Perkins, A. E. (1939). A study of the pH values of the ingesta of the bovine rumen. Journal of Dairy Science, 22(12), 983–991. https://doi.org/10.3168/jds.S00220302(39)92951-6</mixed-citation></citation-alternatives></ref><ref id="cit18"><label>18</label><citation-alternatives><mixed-citation xml:lang="ru">Hungate, R.E. (1942). The culture of Eudiplodinium neglectum with experiments on the digestion of cellulose. The Biological Bulletin, 83(3), 303–319. https://doi.org/10.2307/1538229</mixed-citation><mixed-citation xml:lang="en">Hungate, R.E. (1942). The culture of Eudiplodinium neglectum with experiments on the digestion of cellulose. The Biological Bulletin, 83(3), 303–319. https://doi.org/10.2307/1538229</mixed-citation></citation-alternatives></ref><ref id="cit19"><label>19</label><citation-alternatives><mixed-citation xml:lang="ru">Hungate, R.E. (1943). Further experiments on cellulose digestion by the protozoa in the rumen of cattle. The Biological Bulletin, 84(2), 57–63. https://doi.org/10.2307/1538178</mixed-citation><mixed-citation xml:lang="en">Hungate, R.E. (1943). Further experiments on cellulose digestion by the protozoa in the rumen of cattle. The Biological Bulletin, 84(2), 57–63. https://doi.org/10.2307/1538178</mixed-citation></citation-alternatives></ref><ref id="cit20"><label>20</label><citation-alternatives><mixed-citation xml:lang="ru">Gall, L.S., Thomas, W.E., Loosli, J.K., Huhranen, C.N. (1951). The effect of purified diets upon rumen flora. The Journal of Nutrition, 44(1), 113–122. https://doi.org/10.1093/jn/44.1.113</mixed-citation><mixed-citation xml:lang="en">Gall, L.S., Thomas, W.E., Loosli, J.K., Huhranen, C.N. (1951). The effect of purified diets upon rumen flora. The Journal of Nutrition, 44(1), 113–122. https://doi.org/10.1093/jn/44.1.113</mixed-citation></citation-alternatives></ref><ref id="cit21"><label>21</label><citation-alternatives><mixed-citation xml:lang="ru">Hungate, R.E. (1947). Studies on cellulose fermentation: III. The culture and isolation for cellulose-decomposing bacteria from the rumen of cattle. Journal of Bacteriology, 53(5), 631– 645. https://doi.org/10.1128/jb.53.5.631-645.1947</mixed-citation><mixed-citation xml:lang="en">Hungate, R.E. (1947). Studies on cellulose fermentation: III. The culture and isolation for cellulose-decomposing bacteria from the rumen of cattle. Journal of Bacteriology, 53(5), 631– 645. https://doi.org/10.1128/jb.53.5.631-645.1947</mixed-citation></citation-alternatives></ref><ref id="cit22"><label>22</label><citation-alternatives><mixed-citation xml:lang="ru">Hungate, R.E. (1960). Symposium: Selected topics in microbial ecology. I. Microbial ecology of the rumen. Journal of Bacteriology, 24(4), 353–364. https://doi.org/10.1128/br.24.4.353-364.1960</mixed-citation><mixed-citation xml:lang="en">Hungate, R.E. (1960). Symposium: Selected topics in microbial ecology. I. Microbial ecology of the rumen. Journal of Bacteriology, 24(4), 353–364. https://doi.org/10.1128/br.24.4.353-364.1960</mixed-citation></citation-alternatives></ref><ref id="cit23"><label>23</label><citation-alternatives><mixed-citation xml:lang="ru">Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R. et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269(5223), 496–512. https://doi.org/10.1126/science.7542800</mixed-citation><mixed-citation xml:lang="en">Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R. et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269(5223), 496–512. https://doi.org/10.1126/science.7542800</mixed-citation></citation-alternatives></ref><ref id="cit24"><label>24</label><citation-alternatives><mixed-citation xml:lang="ru">Fraser, C. M., Gocayne, J.D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science, 270(5235), 397–404. https://doi.org/10.1126/science.270.5235.397</mixed-citation><mixed-citation xml:lang="en">Fraser, C. M., Gocayne, J.D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D. et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science, 270(5235), 397–404. https://doi.org/10.1126/science.270.5235.397</mixed-citation></citation-alternatives></ref><ref id="cit25"><label>25</label><citation-alternatives><mixed-citation xml:lang="ru">Baar, C., Eppinger, M., Raddatz, G., Simon, J., Lanz, C., Klimmek, O. et al. (2003). Complete genome sequence and analysis of Wolinella succinogenes. Proceedings of the National Academy of Sciences, 100(20), 11690–11695. https://doi.org/10.1073/pnas.1932838100</mixed-citation><mixed-citation xml:lang="en">Baar, C., Eppinger, M., Raddatz, G., Simon, J., Lanz, C., Klimmek, O. et al. (2003). Complete genome sequence and analysis of Wolinella succinogenes. Proceedings of the National Academy of Sciences, 100(20), 11690–11695. https://doi.org/10.1073/pnas.1932838100</mixed-citation></citation-alternatives></ref><ref id="cit26"><label>26</label><citation-alternatives><mixed-citation xml:lang="ru">Brede, M., Orton, T., Pinior, B., Roch, F.-F., Dzieciol, M., Zwirzitz, B. et al. (2020). PacBio and Illumina MiSeq amplicon sequencing confirm full recovery of the bacterial community after subacute ruminal acidosis challenge in the RUSITEC system. Frontiers in Microbiology, 11, Article 1813. https://doi.org/10.3389/fmicb.2020.01813</mixed-citation><mixed-citation xml:lang="en">Brede, M., Orton, T., Pinior, B., Roch, F.-F., Dzieciol, M., Zwirzitz, B. et al. (2020). PacBio and Illumina MiSeq amplicon sequencing confirm full recovery of the bacterial community after subacute ruminal acidosis challenge in the RUSITEC system. Frontiers in Microbiology, 11, Article 1813. https://doi.org/10.3389/fmicb.2020.01813</mixed-citation></citation-alternatives></ref><ref id="cit27"><label>27</label><citation-alternatives><mixed-citation xml:lang="ru">Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L. et al. (2018). Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 36(4), 359–367. https://doi.org/10.1038/nbt.4110</mixed-citation><mixed-citation xml:lang="en">Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L. et al. (2018). Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 36(4), 359–367. https://doi.org/10.1038/nbt.4110</mixed-citation></citation-alternatives></ref><ref id="cit28"><label>28</label><citation-alternatives><mixed-citation xml:lang="ru">Hess, M., Sczyrba, A., Egan, R., Kim, T.-W., Chokhawala, H., Schroth, G. et al. (2011). Metagenomic discovery of biomassdegrading genes and genomes from cow rumen. Science, 331(6016), 463–467. https://doi.org/10.1126/science.1200387</mixed-citation><mixed-citation xml:lang="en">Hess, M., Sczyrba, A., Egan, R., Kim, T.-W., Chokhawala, H., Schroth, G. et al. (2011). Metagenomic discovery of biomassdegrading genes and genomes from cow rumen. Science, 331(6016), 463–467. https://doi.org/10.1126/science.1200387</mixed-citation></citation-alternatives></ref><ref id="cit29"><label>29</label><citation-alternatives><mixed-citation xml:lang="ru">Ross, E. M., Petrovski, S., Moate, P. J., Hayes, B. J.(2013). Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiology, 13(1), Article 242. https://doi.org/10.1186/1471-2180-13-242</mixed-citation><mixed-citation xml:lang="en">Ross, E. M., Petrovski, S., Moate, P. J., Hayes, B. J.(2013). Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiology, 13(1), Article 242. https://doi.org/10.1186/1471-2180-13-242</mixed-citation></citation-alternatives></ref><ref id="cit30"><label>30</label><citation-alternatives><mixed-citation xml:lang="ru">López-García, P, Gutiérrez-Preciado, A, Krupovic, M, Ciobanu, M, Deschamps, P, Jardillier, L. et al. (2023). Metagenomederived virus-microbe ratios across ecosystems. The ISME Journal, 17(10), 1552–1563. https://doi.org/10.1038/s41396023-01431-y</mixed-citation><mixed-citation xml:lang="en">López-García, P, Gutiérrez-Preciado, A, Krupovic, M, Ciobanu, M, Deschamps, P, Jardillier, L. et al. (2023). Metagenomederived virus-microbe ratios across ecosystems. The ISME Journal, 17(10), 1552–1563. https://doi.org/10.1038/s41396023-01431-y</mixed-citation></citation-alternatives></ref><ref id="cit31"><label>31</label><citation-alternatives><mixed-citation xml:lang="ru">Wallace, R.J., Snelling, T.J., McCartney, C.A., Tapio, I., Strozzi, F. (2017). Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genetics Selection Evolution, 49(1), Article 9. http://doi.org/10.1186/s12711-017-0304-7</mixed-citation><mixed-citation xml:lang="en">Wallace, R.J., Snelling, T.J., McCartney, C.A., Tapio, I., Strozzi, F. (2017). Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genetics Selection Evolution, 49(1), Article 9. http://doi.org/10.1186/s12711-017-0304-7</mixed-citation></citation-alternatives></ref><ref id="cit32"><label>32</label><citation-alternatives><mixed-citation xml:lang="ru">Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A.H., Siu-Ting, K., Hughes, M. (2018). CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software. Frontiers in Microbiology, 25(9), Article 1095. https://doi.org/10.3389/fmicb.2018.01095</mixed-citation><mixed-citation xml:lang="en">Wilkinson, T.J., Huws, S.A., Edwards, J.E., Kingston-Smith, A.H., Siu-Ting, K., Hughes, M. (2018). CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software. Frontiers in Microbiology, 25(9), Article 1095. https://doi.org/10.3389/fmicb.2018.01095</mixed-citation></citation-alternatives></ref><ref id="cit33"><label>33</label><citation-alternatives><mixed-citation xml:lang="ru">Khairunisa, B. H., Heryakusuma, C., Ike, K., Mukhopadhyay, B., Susanti, D. (2023). Evolving understanding of rumen methanogen ecophysiology. Frontiers in Microbiology, 14, Article 1296008. https://doi.org/10.3389/fmicb.2023.1296008</mixed-citation><mixed-citation xml:lang="en">Khairunisa, B. H., Heryakusuma, C., Ike, K., Mukhopadhyay, B., Susanti, D. (2023). Evolving understanding of rumen methanogen ecophysiology. Frontiers in Microbiology, 14, Article 1296008. https://doi.org/10.3389/fmicb.2023.1296008</mixed-citation></citation-alternatives></ref><ref id="cit34"><label>34</label><citation-alternatives><mixed-citation xml:lang="ru">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(2), 115–132. https://doi.org/10.1080/19490976.2018.1505176</mixed-citation><mixed-citation xml:lang="en">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(2), 115–132. https://doi.org/10.1080/19490976.2018.1505176</mixed-citation></citation-alternatives></ref><ref id="cit35"><label>35</label><citation-alternatives><mixed-citation xml:lang="ru">Lilian, M., Rawlynce, B., Charles, G., Felix, K. (2023). Potential role of rumen bacteria in modulating milk production and composition of admixed dairy cows. Letters in Applied Microbiology, 76(2), Article ovad007. https://doi.org/10.1093/lambio/ovad007</mixed-citation><mixed-citation xml:lang="en">Lilian, M., Rawlynce, B., Charles, G., Felix, K. (2023). Potential role of rumen bacteria in modulating milk production and composition of admixed dairy cows. Letters in Applied Microbiology, 76(2), Article ovad007. https://doi.org/10.1093/lambio/ovad007</mixed-citation></citation-alternatives></ref><ref id="cit36"><label>36</label><citation-alternatives><mixed-citation xml:lang="ru">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(14), 4697–4710. https://doi.org/10.1128/AEM.00720-15</mixed-citation><mixed-citation xml:lang="en">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(14), 4697–4710. https://doi.org/10.1128/AEM.00720-15</mixed-citation></citation-alternatives></ref><ref id="cit37"><label>37</label><citation-alternatives><mixed-citation xml:lang="ru">Kameshwar, A. K. S., Qin, W. (2018). Genome wide analysis reveals the extrinsic cellulolytic and biohydrogen generating abilities of Neocallimastigomycota fungi. Journal of Genomics, 6, 74–87. https://doi.org/10.7150/jgen.25648</mixed-citation><mixed-citation xml:lang="en">Kameshwar, A. K. S., Qin, W. (2018). Genome wide analysis reveals the extrinsic cellulolytic and biohydrogen generating abilities of Neocallimastigomycota fungi. Journal of Genomics, 6, 74–87. https://doi.org/10.7150/jgen.25648</mixed-citation></citation-alternatives></ref><ref id="cit38"><label>38</label><citation-alternatives><mixed-citation xml:lang="ru">Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Abecia, L. et al. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports, 5(1), Article 14567. https://doi.org/10.1038/srep14567</mixed-citation><mixed-citation xml:lang="en">Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Abecia, L. et al. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports, 5(1), Article 14567. https://doi.org/10.1038/srep14567</mixed-citation></citation-alternatives></ref><ref id="cit39"><label>39</label><citation-alternatives><mixed-citation xml:lang="ru">Han, Z., Willer, T., Li, L., Pielsticker, C., Rychlik, I., Velge, P. et al. (2017). Influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens. Infection and Immunity, 85(11), Article iai.00380–17. https://doi.org/10.1128/iai.00380-17</mixed-citation><mixed-citation xml:lang="en">Han, Z., Willer, T., Li, L., Pielsticker, C., Rychlik, I., Velge, P. et al. (2017). Influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens. Infection and Immunity, 85(11), Article iai.00380–17. https://doi.org/10.1128/iai.00380-17</mixed-citation></citation-alternatives></ref><ref id="cit40"><label>40</label><citation-alternatives><mixed-citation xml:lang="ru">Kraimi, N., Dawkins, M., Gebhardt-Henrich, S. G., Velge, P., Rychlik, I., Volf, J.et al. (2019). Influence of the microbiotagut-brain axis on behavior and welfare in farm animals: A review. Physiology and Behavior, 210, Article 112658. https://doi.org/10.1016/j.physbeh.2019.112658</mixed-citation><mixed-citation xml:lang="en">Kraimi, N., Dawkins, M., Gebhardt-Henrich, S. G., Velge, P., Rychlik, I., Volf, J.et al. (2019). Influence of the microbiotagut-brain axis on behavior and welfare in farm animals: A review. Physiology and Behavior, 210, Article 112658. https://doi.org/10.1016/j.physbeh.2019.112658</mixed-citation></citation-alternatives></ref><ref id="cit41"><label>41</label><citation-alternatives><mixed-citation xml:lang="ru">Ji, S., Zhang, H., Yan, H., Azarfar, A., Shi, H., Alugongo, G. et al. (2017). Comparison of rumen bacteria distribution in original rumen digesta, rumen liquid and solid fractions in lactating Holstein cows. Journal of Animal Science and Biotechnology, 8(1), Article 16. https://doi.org/10.1186/s40104-017-0142-z</mixed-citation><mixed-citation xml:lang="en">Ji, S., Zhang, H., Yan, H., Azarfar, A., Shi, H., Alugongo, G. et al. (2017). Comparison of rumen bacteria distribution in original rumen digesta, rumen liquid and solid fractions in lactating Holstein cows. Journal of Animal Science and Biotechnology, 8(1), Article 16. https://doi.org/10.1186/s40104-017-0142-z</mixed-citation></citation-alternatives></ref><ref id="cit42"><label>42</label><citation-alternatives><mixed-citation xml:lang="ru">De Mulder, T., Goossens, K., Peiren, N., Vandaele, L., Haegeman, A., De Tender, C. et al. (2016). Exploring the methanogen and bacterial communities of rumen environments: Solid adherent, fluid and epimural. FEMS Microbiology Ecology, 93(3), Article fiw251. https://doi.org/10.1093/femsec/fiw251</mixed-citation><mixed-citation xml:lang="en">De Mulder, T., Goossens, K., Peiren, N., Vandaele, L., Haegeman, A., De Tender, C. et al. (2016). Exploring the methanogen and bacterial communities of rumen environments: Solid adherent, fluid and epimural. FEMS Microbiology Ecology, 93(3), Article fiw251. https://doi.org/10.1093/femsec/fiw251</mixed-citation></citation-alternatives></ref><ref id="cit43"><label>43</label><citation-alternatives><mixed-citation xml:lang="ru">Na, S. W., Guan, L. L. (2022). Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency. Animal Nutrition, 10, 41–53. https://doi.org/10.1016/j.aninu.2022.04.002</mixed-citation><mixed-citation xml:lang="en">Na, S. W., Guan, L. L. (2022). Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency. Animal Nutrition, 10, 41–53. https://doi.org/10.1016/j.aninu.2022.04.002</mixed-citation></citation-alternatives></ref><ref id="cit44"><label>44</label><citation-alternatives><mixed-citation xml:lang="ru">Schmitz-Esser, S. (2021). The rumen epithelial microbiota: Possible gatekeepers of the rumen epithelium and its potential contributions to epithelial barrier function and animal health and performance. Meat and Muscle Biology, 4(2), Article 19. https://doi.org/10.22175/mmb.11672</mixed-citation><mixed-citation xml:lang="en">Schmitz-Esser, S. (2021). The rumen epithelial microbiota: Possible gatekeepers of the rumen epithelium and its potential contributions to epithelial barrier function and animal health and performance. Meat and Muscle Biology, 4(2), Article 19. https://doi.org/10.22175/mmb.11672</mixed-citation></citation-alternatives></ref><ref id="cit45"><label>45</label><citation-alternatives><mixed-citation xml:lang="ru">Petri, R. M., Neubauer, V., Humer, E., Kröger, I., Reisinger, N., Zebeli, Q. (2020). Feed additives differentially impact the epimural microbiota and host epithelial gene expression of the bovine rumen fed diets rich in concentrates. Frontiers in Microbiology, 11, Article 119. https://doi.org/10.3389/fmicb.2020.00119</mixed-citation><mixed-citation xml:lang="en">Petri, R. M., Neubauer, V., Humer, E., Kröger, I., Reisinger, N., Zebeli, Q. (2020). Feed additives differentially impact the epimural microbiota and host epithelial gene expression of the bovine rumen fed diets rich in concentrates. Frontiers in Microbiology, 11, Article 119. https://doi.org/10.3389/fmicb.2020.00119</mixed-citation></citation-alternatives></ref><ref id="cit46"><label>46</label><citation-alternatives><mixed-citation xml:lang="ru">de Menezes, A. B., Lewis, E., O’Donovan, M., O’Neill, B. F., Clipson, N., Doyle, E. M. (2011). Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiology Ecology, 78(2), 256–265. https://doi.org/10.1111/j.1574-6941.2011.01151.x</mixed-citation><mixed-citation xml:lang="en">de Menezes, A. B., Lewis, E., O’Donovan, M., O’Neill, B. F., Clipson, N., Doyle, E. M. (2011). Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiology Ecology, 78(2), 256–265. https://doi.org/10.1111/j.1574-6941.2011.01151.x</mixed-citation></citation-alternatives></ref><ref id="cit47"><label>47</label><citation-alternatives><mixed-citation xml:lang="ru">Durso, L. M., Miller, D. N., Schmidt, T. B., Callaway, T. (2017). Tracking bacteria through the entire gastrointestinal tract of a beef steer. Agricultural and Environmental Letters, 2(1), Article 170016. https://doi.org/10.2134/ael2017.05.0016</mixed-citation><mixed-citation xml:lang="en">Durso, L. M., Miller, D. N., Schmidt, T. B., Callaway, T. (2017). Tracking bacteria through the entire gastrointestinal tract of a beef steer. Agricultural and Environmental Letters, 2(1), Article 170016. https://doi.org/10.2134/ael2017.05.0016</mixed-citation></citation-alternatives></ref><ref id="cit48"><label>48</label><citation-alternatives><mixed-citation xml:lang="ru">Castillo-Gonzalez, A.R., Burrola-Barraza, M.E., Viveros, J.D. (2014). Rumen microorganisms and fermentation. Archivos de Medicina Veterinaria, 46(3), 349–361. https://doi.org/10.4067/S0301-732X2014000300003</mixed-citation><mixed-citation xml:lang="en">Castillo-Gonzalez, A.R., Burrola-Barraza, M.E., Viveros, J.D. (2014). Rumen microorganisms and fermentation. Archivos de Medicina Veterinaria, 46(3), 349–361. https://doi.org/10.4067/S0301-732X2014000300003</mixed-citation></citation-alternatives></ref><ref id="cit49"><label>49</label><citation-alternatives><mixed-citation xml:lang="ru">Ziemer, C.J.(2013). Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides. Applied and Environmental Microbiology, 80(2), 574–585. https://doi.org/10.1128/AEM.03016-13</mixed-citation><mixed-citation xml:lang="en">Ziemer, C.J.(2013). Newly cultured bacteria with broad diversity isolated from eight-week continuous culture enrichments of cow feces on complex polysaccharides. Applied and Environmental Microbiology, 80(2), 574–585. https://doi.org/10.1128/AEM.03016-13</mixed-citation></citation-alternatives></ref><ref id="cit50"><label>50</label><citation-alternatives><mixed-citation xml:lang="ru">Koike, S., Kobayashi, Y. (2009). Fibrolytic rumen bacteria: Their ecology and functions. Asian-Australasian Journal of Animal Sciences, 22(1), 131–138. https://doi.org/10.5713/ajas.2009.r.01</mixed-citation><mixed-citation xml:lang="en">Koike, S., Kobayashi, Y. (2009). Fibrolytic rumen bacteria: Their ecology and functions. Asian-Australasian Journal of Animal Sciences, 22(1), 131–138. https://doi.org/10.5713/ajas.2009.r.01</mixed-citation></citation-alternatives></ref><ref id="cit51"><label>51</label><citation-alternatives><mixed-citation xml:lang="ru">Hungate, R.E. (1950). The anaerobic mesophilic cellulolytic bacteria. Bacteriological Reviews, 14(1), 1–49. https://doi.org/10.1128/br.14.1.1-49.1950</mixed-citation><mixed-citation xml:lang="en">Hungate, R.E. (1950). The anaerobic mesophilic cellulolytic bacteria. Bacteriological Reviews, 14(1), 1–49. https://doi.org/10.1128/br.14.1.1-49.1950</mixed-citation></citation-alternatives></ref><ref id="cit52"><label>52</label><citation-alternatives><mixed-citation xml:lang="ru">Russell, J.B., Muck, R.E., Weimer, P.J.(2009). Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen. FEMS Microbiology Ecology, 67(2), 183–197. https://doi.org/10.1111/j.1574-6941.2008.00633.x</mixed-citation><mixed-citation xml:lang="en">Russell, J.B., Muck, R.E., Weimer, P.J.(2009). Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen. FEMS Microbiology Ecology, 67(2), 183–197. https://doi.org/10.1111/j.1574-6941.2008.00633.x</mixed-citation></citation-alternatives></ref><ref id="cit53"><label>53</label><citation-alternatives><mixed-citation xml:lang="ru">Ratti, R. P., Botta, L. S., Sakamoto, I. K., Silva, E. L., Varesche, M. B. A. (2014). Production of H2 from cellulose by rumen microorganisms: Effects of inocula pre-treatment and enzymatic hydrolysis. Biotechnology Letters, 36(3), 537–546. https://doi.org/10.1007/s10529–013–1395-z</mixed-citation><mixed-citation xml:lang="en">Ratti, R. P., Botta, L. S., Sakamoto, I. K., Silva, E. L., Varesche, M. B. A. (2014). Production of H2 from cellulose by rumen microorganisms: Effects of inocula pre-treatment and enzymatic hydrolysis. Biotechnology Letters, 36(3), 537–546. https://doi.org/10.1007/s10529–013–1395-z</mixed-citation></citation-alternatives></ref><ref id="cit54"><label>54</label><citation-alternatives><mixed-citation xml:lang="ru">Odenyo, A.A., Mackie, R.I., Stahl, D.A., White, B.A. (1994). The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: Development of probes for Ruminococcus species and evidence for bacteriocin production. Applied and Environmental Microbiology, 60(10), 3688–3696. https://doi.org/10.1128/aem.60.10.3688–3696.1994</mixed-citation><mixed-citation xml:lang="en">Odenyo, A.A., Mackie, R.I., Stahl, D.A., White, B.A. (1994). The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: Development of probes for Ruminococcus species and evidence for bacteriocin production. Applied and Environmental Microbiology, 60(10), 3688–3696. https://doi.org/10.1128/aem.60.10.3688–3696.1994</mixed-citation></citation-alternatives></ref><ref id="cit55"><label>55</label><citation-alternatives><mixed-citation xml:lang="ru">Fernando, S. C., Purvis II, H. T., Najar, F. Z., Sukharnikov, L. O., Krehbiel, C. R., Nagaraja, T. G. et al. (2010). Rumen microbial population dynamics during adaptation to a highgrain diet. Applied and Environmental Microbiology, 76(22), 7482–7490. https://doi.org/10.1128/AEM.00388-10</mixed-citation><mixed-citation xml:lang="en">Fernando, S. C., Purvis II, H. T., Najar, F. Z., Sukharnikov, L. O., Krehbiel, C. R., Nagaraja, T. G. et al. (2010). Rumen microbial population dynamics during adaptation to a highgrain diet. Applied and Environmental Microbiology, 76(22), 7482–7490. https://doi.org/10.1128/AEM.00388-10</mixed-citation></citation-alternatives></ref><ref id="cit56"><label>56</label><citation-alternatives><mixed-citation xml:lang="ru">Duskova, 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(2), 159–163. https://doi.org/10.1046/j.1472765x.2001.00970.x</mixed-citation><mixed-citation xml:lang="en">Duskova, 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(2), 159–163. https://doi.org/10.1046/j.1472765x.2001.00970.x</mixed-citation></citation-alternatives></ref><ref id="cit57"><label>57</label><citation-alternatives><mixed-citation xml:lang="ru">Chen, Y., Oba, M., Guan, L. L. (2012). Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis. Veterinary Microbiology, 159(3–4), 451–459. https://doi.org/10.1016/j.vetmic.2012.04.032</mixed-citation><mixed-citation xml:lang="en">Chen, Y., Oba, M., Guan, L. L. (2012). Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis. Veterinary Microbiology, 159(3–4), 451–459. https://doi.org/10.1016/j.vetmic.2012.04.032</mixed-citation></citation-alternatives></ref><ref id="cit58"><label>58</label><citation-alternatives><mixed-citation xml:lang="ru">Santos, G. T., Lima, L. S., Schogor, A. L. B., Romero, J.V., De Marchi, F. E., Grande, P. A. et al. (2014). Citrus pulp as a dietary source of antioxidants for lactating holstein cows fed highly polyunsaturated fatty acid diets. Asian-Australasian Journal of Animal Sciences, 27(8), 1104–1113. https://doi.org/10.5713/ajas.2013.13836</mixed-citation><mixed-citation xml:lang="en">Santos, G. T., Lima, L. S., Schogor, A. L. B., Romero, J.V., De Marchi, F. E., Grande, P. A. et al. (2014). Citrus pulp as a dietary source of antioxidants for lactating holstein cows fed highly polyunsaturated fatty acid diets. Asian-Australasian Journal of Animal Sciences, 27(8), 1104–1113. https://doi.org/10.5713/ajas.2013.13836</mixed-citation></citation-alternatives></ref><ref id="cit59"><label>59</label><citation-alternatives><mixed-citation xml:lang="ru">de Almeida, P. N. M., Duarte, E. R., Abrão, F. O., Freitas, C. E. S., Geraseev, L. C., Rosa, C. A. (2012). Aerobic fungi in the rumen fluid from dairy cattle fed different sources of forage. Revista Brasileira de Zootecnia, 41(11), 2336–2342. https://doi.org/10.1590/S1516-35982012001100006</mixed-citation><mixed-citation xml:lang="en">de Almeida, P. N. M., Duarte, E. R., Abrão, F. O., Freitas, C. E. S., Geraseev, L. C., Rosa, C. A. (2012). Aerobic fungi in the rumen fluid from dairy cattle fed different sources of forage. Revista Brasileira de Zootecnia, 41(11), 2336–2342. https://doi.org/10.1590/S1516-35982012001100006</mixed-citation></citation-alternatives></ref><ref id="cit60"><label>60</label><citation-alternatives><mixed-citation xml:lang="ru">Gruninger, R. J., Puniya, A. K., Callaghan, T. M., Edwards, J.E., Youssef, N., Dagar, S. S. et al. (2014). Anaerobic fungi (phylum Neocallimastigomycota): Advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiology Ecology, 90(1), 1–17. https://doi.org/10.1111/1574-6941.12383</mixed-citation><mixed-citation xml:lang="en">Gruninger, R. J., Puniya, A. K., Callaghan, T. M., Edwards, J.E., Youssef, N., Dagar, S. S. et al. (2014). Anaerobic fungi (phylum Neocallimastigomycota): Advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiology Ecology, 90(1), 1–17. https://doi.org/10.1111/1574-6941.12383</mixed-citation></citation-alternatives></ref><ref id="cit61"><label>61</label><citation-alternatives><mixed-citation xml:lang="ru">Wang, R., He, S., Huang, D., He, S., Guo, T., Chen, T. et al. (2023). Differences in composition and diversity of rumen fungi in buff lo fed different diets. Animal Biotechnology, 34(9), 5075–5086. https://doi.org/10.1080/10495398.2023.2276974</mixed-citation><mixed-citation xml:lang="en">Wang, R., He, S., Huang, D., He, S., Guo, T., Chen, T. et al. (2023). Differences in composition and diversity of rumen fungi in buff lo fed different diets. Animal Biotechnology, 34(9), 5075–5086. https://doi.org/10.1080/10495398.2023.2276974</mixed-citation></citation-alternatives></ref><ref id="cit62"><label>62</label><citation-alternatives><mixed-citation xml:lang="ru">Li, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B. et al. (2019). Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome, 7(1), Article 92. https://doi.org/10.1186/s40168-019-0699-1</mixed-citation><mixed-citation xml:lang="en">Li, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B. et al. (2019). Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome, 7(1), Article 92. https://doi.org/10.1186/s40168-019-0699-1</mixed-citation></citation-alternatives></ref><ref id="cit63"><label>63</label><citation-alternatives><mixed-citation xml:lang="ru">Lin, C., Raskin, L., Stahl, D. A. (2006). Microbial community structure in gastrointestinal tracts of domestic animals: Comparative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiology Ecology, 22(4), 281–294. https://doi.org/10.1111/j.1574-6941.1997.tb00380.x</mixed-citation><mixed-citation xml:lang="en">Lin, C., Raskin, L., Stahl, D. A. (2006). Microbial community structure in gastrointestinal tracts of domestic animals: Comparative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiology Ecology, 22(4), 281–294. https://doi.org/10.1111/j.1574-6941.1997.tb00380.x</mixed-citation></citation-alternatives></ref><ref id="cit64"><label>64</label><citation-alternatives><mixed-citation xml:lang="ru">Hook, S. E., Wright, A.-D. G., McBride, B. W. (2010). Methanogens: Methane producers of the rumen and mitigation strategies. Archaea, 2010, Article 945785. https://doi.org/10.1155/2010/945785</mixed-citation><mixed-citation xml:lang="en">Hook, S. E., Wright, A.-D. G., McBride, B. W. (2010). Methanogens: Methane producers of the rumen and mitigation strategies. Archaea, 2010, Article 945785. https://doi.org/10.1155/2010/945785</mixed-citation></citation-alternatives></ref><ref id="cit65"><label>65</label><citation-alternatives><mixed-citation xml:lang="ru">Leahy, S. C., Kelly, W. J., Ronimus, R. S., Wedlock, N., Altermann, E., Attwood, G. T. (2013). Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal, 7(Suppl 2), 235–243. https://doi.org/10.1017/S1751731113000700</mixed-citation><mixed-citation xml:lang="en">Leahy, S. C., Kelly, W. J., Ronimus, R. S., Wedlock, N., Altermann, E., Attwood, G. T. (2013). Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal, 7(Suppl 2), 235–243. https://doi.org/10.1017/S1751731113000700</mixed-citation></citation-alternatives></ref><ref id="cit66"><label>66</label><citation-alternatives><mixed-citation xml:lang="ru">Goopy, J.P., Donaldson, A., Hegarty, R., Vercoe, P. E., Haynes, F., Barnett, M. et al. (2014). Low-methane yield sheep have smaller rumens and shorter rumen retention time. British Journal of Nutrition, 111(4), 578–585. https://doi.org/10.1017/S0007114513002936</mixed-citation><mixed-citation xml:lang="en">Goopy, J.P., Donaldson, A., Hegarty, R., Vercoe, P. E., Haynes, F., Barnett, M. et al. (2014). Low-methane yield sheep have smaller rumens and shorter rumen retention time. British Journal of Nutrition, 111(4), 578–585. https://doi.org/10.1017/S0007114513002936</mixed-citation></citation-alternatives></ref><ref id="cit67"><label>67</label><citation-alternatives><mixed-citation xml:lang="ru">FAO. (2023). Pathways towards lower emissions — A global assessment of the greenhouse gas emissions and mitigation options from livestock agrifood systems. Rome, 2023. https://doi.org/10.4060/cc9029en</mixed-citation><mixed-citation xml:lang="en">FAO. (2023). Pathways towards lower emissions — A global assessment of the greenhouse gas emissions and mitigation options from livestock agrifood systems. Rome, 2023. https://doi.org/10.4060/cc9029en</mixed-citation></citation-alternatives></ref><ref id="cit68"><label>68</label><citation-alternatives><mixed-citation xml:lang="ru">Khairunisa, B. H., Heryakusuma, C., Ike, K., Mukhopadhyay, B., Susanti, D. (2023). Evolving understanding of rumen methanogen ecophysiology. Frontiers in Microbiology, 14, Article 1296008. https://doi.org/10.3389/fmicb.2023.1296008</mixed-citation><mixed-citation xml:lang="en">Khairunisa, B. H., Heryakusuma, C., Ike, K., Mukhopadhyay, B., Susanti, D. (2023). Evolving understanding of rumen methanogen ecophysiology. Frontiers in Microbiology, 14, Article 1296008. https://doi.org/10.3389/fmicb.2023.1296008</mixed-citation></citation-alternatives></ref><ref id="cit69"><label>69</label><citation-alternatives><mixed-citation xml:lang="ru">Tsai, B. (2007). Penetration of nonenveloped viruses into the cytoplasm. Annual Review of Cell and Developmental Biology, 23(1), 23–43. https://doi.org/10.1146/annurev.cellbio.23.090506.123454</mixed-citation><mixed-citation xml:lang="en">Tsai, B. (2007). Penetration of nonenveloped viruses into the cytoplasm. Annual Review of Cell and Developmental Biology, 23(1), 23–43. https://doi.org/10.1146/annurev.cellbio.23.090506.123454</mixed-citation></citation-alternatives></ref><ref id="cit70"><label>70</label><citation-alternatives><mixed-citation xml:lang="ru">Paynter, M.J.B., Ewert, D.L., Chalupa, W. (1969). Some morphological types of bacteriophages in bovine rumen contents. Applied Microbiology, 18(5), 942–943. https://doi.org/10.1128/AM.18.5.942-943.1969</mixed-citation><mixed-citation xml:lang="en">Paynter, M.J.B., Ewert, D.L., Chalupa, W. (1969). Some morphological types of bacteriophages in bovine rumen contents. Applied Microbiology, 18(5), 942–943. https://doi.org/10.1128/AM.18.5.942-943.1969</mixed-citation></citation-alternatives></ref><ref id="cit71"><label>71</label><citation-alternatives><mixed-citation xml:lang="ru">Klieve, A.V., Swain, R.A. (1993). Estimation of ruminal bacteriophage numbers by pulsed-field gel electrophoresis and laser densitometry. Applied and Environmental Microbiology, 59(7), 2299–2303. https://doi.org/10.1128/aem.59.7.2299-2303.1993</mixed-citation><mixed-citation xml:lang="en">Klieve, A.V., Swain, R.A. (1993). Estimation of ruminal bacteriophage numbers by pulsed-field gel electrophoresis and laser densitometry. Applied and Environmental Microbiology, 59(7), 2299–2303. https://doi.org/10.1128/aem.59.7.2299-2303.1993</mixed-citation></citation-alternatives></ref><ref id="cit72"><label>72</label><citation-alternatives><mixed-citation xml:lang="ru">Yan, M., Yu, Z. (2024). Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits. Microbiome, 12(1), Article 82. https://doi.org/10.1186/s40168-024-01791-3</mixed-citation><mixed-citation xml:lang="en">Yan, M., Yu, Z. (2024). Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits. Microbiome, 12(1), Article 82. https://doi.org/10.1186/s40168-024-01791-3</mixed-citation></citation-alternatives></ref><ref id="cit73"><label>73</label><citation-alternatives><mixed-citation xml:lang="ru">Liu, X., Tang, Y., Chen, H., Liu, J.-X., Sun, H.-Z. (2025). Rumen DNA virome and its relationship with feed efficiency in dairy cows. Microbiome, 13(1), Article 14. https://doi.org/10.1186/s40168-024-02019-0</mixed-citation><mixed-citation xml:lang="en">Liu, X., Tang, Y., Chen, H., Liu, J.-X., Sun, H.-Z. (2025). Rumen DNA virome and its relationship with feed efficiency in dairy cows. Microbiome, 13(1), Article 14. https://doi.org/10.1186/s40168-024-02019-0</mixed-citation></citation-alternatives></ref><ref id="cit74"><label>74</label><citation-alternatives><mixed-citation xml:lang="ru">Zhernov, Y.V., Konstantinov, A.I., Zherebker, A., Nikolaev, E., Orlov, A,. Savinykh, M.I. et al. (2021). Antiviral activity of natural humic substances and shilajit materials against HIV-1: Relation to structure. Environmental Research, 193, Article 110312. https://doi.org/10.1016/j.envres.2020.110312</mixed-citation><mixed-citation xml:lang="en">Zhernov, Y.V., Konstantinov, A.I., Zherebker, A., Nikolaev, E., Orlov, A,. Savinykh, M.I. et al. (2021). Antiviral activity of natural humic substances and shilajit materials against HIV-1: Relation to structure. Environmental Research, 193, Article 110312. https://doi.org/10.1016/j.envres.2020.110312</mixed-citation></citation-alternatives></ref><ref id="cit75"><label>75</label><citation-alternatives><mixed-citation xml:lang="ru">Sato, Y. (2025). Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits. ISME Communications, 5(1), Article ycaf021. https://doi.org/10.1093/ismeco/ycaf021</mixed-citation><mixed-citation xml:lang="en">Sato, Y. (2025). Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits. ISME Communications, 5(1), Article ycaf021. https://doi.org/10.1093/ismeco/ycaf021</mixed-citation></citation-alternatives></ref><ref id="cit76"><label>76</label><citation-alternatives><mixed-citation xml:lang="ru">Sato, Y., Takebe, H., Tominaga, K., Yasuda, J., Kumagai, H., Hirooka, H. et al. (2025). A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals. Applied and Environmental Microbiology, 90(1), Article e0158123. https://doi.org/10.1128/aem.01581-23</mixed-citation><mixed-citation xml:lang="en">Sato, Y., Takebe, H., Tominaga, K., Yasuda, J., Kumagai, H., Hirooka, H. et al. (2025). A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals. Applied and Environmental Microbiology, 90(1), Article e0158123. https://doi.org/10.1128/aem.01581-23</mixed-citation></citation-alternatives></ref><ref id="cit77"><label>77</label><citation-alternatives><mixed-citation xml:lang="ru">Indikova, I., Humphrey, T. J., Hilbert, F. (2015). Survival with a helping hand: Campylobacter and microbiota. Frontiers in Microbiology, 6, Article 1266. https://doi.org/10.3389/fmicb.2015.01266</mixed-citation><mixed-citation xml:lang="en">Indikova, I., Humphrey, T. J., Hilbert, F. (2015). Survival with a helping hand: Campylobacter and microbiota. Frontiers in Microbiology, 6, Article 1266. https://doi.org/10.3389/fmicb.2015.01266</mixed-citation></citation-alternatives></ref><ref id="cit78"><label>78</label><citation-alternatives><mixed-citation xml:lang="ru">Olofsson, J., Axelsson-Olsson, D., Brudin, L., Olsen, B., Ellström, P. (2013). Campylobacter jejuni actively invades the amoeba acanthamoeba polyphaga and survives within non digestive vacuoles. PLoS ONE, 8(11), Article e78873. https://doi.org/10.1371/journal.pone.0078873</mixed-citation><mixed-citation xml:lang="en">Olofsson, J., Axelsson-Olsson, D., Brudin, L., Olsen, B., Ellström, P. (2013). Campylobacter jejuni actively invades the amoeba acanthamoeba polyphaga and survives within non digestive vacuoles. PLoS ONE, 8(11), Article e78873. https://doi.org/10.1371/journal.pone.0078873</mixed-citation></citation-alternatives></ref><ref id="cit79"><label>79</label><citation-alternatives><mixed-citation xml:lang="ru">Sahin, O., Fitzgerald, C., Stroika, S., Zhao, S., Sippy, R. J., Kwan, P. et al. (2012). Molecular evidence for zoonotic transmission of an emergent, highly pathogenic Campylobacter jejuni clone in the United States. Journal of Clinical Microbiology, 50(3), 680–687. https://doi.org/10.1128/JCM.06167-11</mixed-citation><mixed-citation xml:lang="en">Sahin, O., Fitzgerald, C., Stroika, S., Zhao, S., Sippy, R. J., Kwan, P. et al. (2012). Molecular evidence for zoonotic transmission of an emergent, highly pathogenic Campylobacter jejuni clone in the United States. Journal of Clinical Microbiology, 50(3), 680–687. https://doi.org/10.1128/JCM.06167-11</mixed-citation></citation-alternatives></ref><ref id="cit80"><label>80</label><citation-alternatives><mixed-citation xml:lang="ru">Cedrola, F, Senra, M.V.X., Rossi, M.F., Fregulia, P., D’Agosto, M., Dias, R.J.P. (2020). Trichostomatid ciliates (Alveolata, Ciliophora, Trichostomatia) systematics and diversity: Past, present, and future. (2020). Frontiers in Microbiology, 10, Article 2967. https://doi.org/10.3389/fmicb.2019.02967</mixed-citation><mixed-citation xml:lang="en">Cedrola, F, Senra, M.V.X., Rossi, M.F., Fregulia, P., D’Agosto, M., Dias, R.J.P. (2020). Trichostomatid ciliates (Alveolata, Ciliophora, Trichostomatia) systematics and diversity: Past, present, and future. (2020). Frontiers in Microbiology, 10, Article 2967. https://doi.org/10.3389/fmicb.2019.02967</mixed-citation></citation-alternatives></ref><ref id="cit81"><label>81</label><citation-alternatives><mixed-citation xml:lang="ru">Cedrola, F., Bordim, S. C., Arcuri, P. B., da Costa Carneiro, J., Dias, R.J.P. (2024). Rumen ciliates (Ciliophora, Trichostomatia) in Brazilian domestic cattle feeding on diets with crescent urea levels. European Journal of Protistology, 93, Article 126063. https://doi.org/10.1016/j.ejop.2024.126063</mixed-citation><mixed-citation xml:lang="en">Cedrola, F., Bordim, S. C., Arcuri, P. B., da Costa Carneiro, J., Dias, R.J.P. (2024). Rumen ciliates (Ciliophora, Trichostomatia) in Brazilian domestic cattle feeding on diets with crescent urea levels. European Journal of Protistology, 93, Article 126063. https://doi.org/10.1016/j.ejop.2024.126063</mixed-citation></citation-alternatives></ref><ref id="cit82"><label>82</label><citation-alternatives><mixed-citation xml:lang="ru">Williams, C.L., Thomas, B.J., McEwan, N.R., Stevens, P.R., Creevey, C.J., Huws, S.A. (2020). Rumen protozoa play a significant role in fungal predation and plant carbohydrate breakdown. Frontiers in Microbiology, 11, Article 720. https://doi.org/10.3389/fmicb.2020.00720</mixed-citation><mixed-citation xml:lang="en">Williams, C.L., Thomas, B.J., McEwan, N.R., Stevens, P.R., Creevey, C.J., Huws, S.A. (2020). Rumen protozoa play a significant role in fungal predation and plant carbohydrate breakdown. Frontiers in Microbiology, 11, Article 720. https://doi.org/10.3389/fmicb.2020.00720</mixed-citation></citation-alternatives></ref><ref id="cit83"><label>83</label><citation-alternatives><mixed-citation xml:lang="ru">Devillard, E., Bera-Maillet, C., Flint, H.J, Scott, K.P., Newbold, J., Wallace, J.et al. (2003). Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydratebinding module that binds to cellulose. Biochemical Journal, 373(Pt 2), 495–503. https://doi.org/10.1042/bj20021784</mixed-citation><mixed-citation xml:lang="en">Devillard, E., Bera-Maillet, C., Flint, H.J, Scott, K.P., Newbold, J., Wallace, J.et al. (2003). Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydratebinding module that binds to cellulose. Biochemical Journal, 373(Pt 2), 495–503. https://doi.org/10.1042/bj20021784</mixed-citation></citation-alternatives></ref><ref id="cit84"><label>84</label><citation-alternatives><mixed-citation xml:lang="ru">Andersen, T.O., Altshuler, I., de León, A.V.-P., Walter, J.M., McGovern, E., Keogh, K. et al. (2023). Metabolic influence of core ciliates within the rumen microbiome. The ISME Journal, 17(7), 1128–1140. https://doi.org/10.1038/s41396023-01407-y</mixed-citation><mixed-citation xml:lang="en">Andersen, T.O., Altshuler, I., de León, A.V.-P., Walter, J.M., McGovern, E., Keogh, K. et al. (2023). Metabolic influence of core ciliates within the rumen microbiome. The ISME Journal, 17(7), 1128–1140. https://doi.org/10.1038/s41396023-01407-y</mixed-citation></citation-alternatives></ref><ref id="cit85"><label>85</label><citation-alternatives><mixed-citation xml:lang="ru">Park, T,, Mao, H., Yu, Z. (2019). Inhibition of rumen protozoa by specific inhibitors of lysozyme and peptidases in vitro. Frontiers in Microbiology, 10, Article 2822. https://doi.org/10.3389/fmicb.2019.02822</mixed-citation><mixed-citation xml:lang="en">Park, T,, Mao, H., Yu, Z. (2019). Inhibition of rumen protozoa by specific inhibitors of lysozyme and peptidases in vitro. Frontiers in Microbiology, 10, Article 2822. https://doi.org/10.3389/fmicb.2019.02822</mixed-citation></citation-alternatives></ref><ref id="cit86"><label>86</label><citation-alternatives><mixed-citation xml:lang="ru">Wang, L., Abu-Doleh, A., Plank, J., Catalyurek, U.V., Firkins, J.L., Yu. Z. (2019). The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features. BMC Genomics, 20(1), Article 1008. https://doi.org/10.1186/s12864-019-6382-x</mixed-citation><mixed-citation xml:lang="en">Wang, L., Abu-Doleh, A., Plank, J., Catalyurek, U.V., Firkins, J.L., Yu. Z. (2019). The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features. BMC Genomics, 20(1), Article 1008. https://doi.org/10.1186/s12864-019-6382-x</mixed-citation></citation-alternatives></ref><ref id="cit87"><label>87</label><citation-alternatives><mixed-citation xml:lang="ru">Stefanska, B., Sroka, J., Katzer, F., Golinski, P., Nowak, W. (2020). The effect of probiotics, phytobiotics and their combination as feed additives in the diet of dairy calves on performance, rumen fermentation and blood metabolites during the preweaning period. Animal Feed Science and Technology, 272, Article 114728. https://doi.org/10.1016/j.anifeedsci.2020.114738</mixed-citation><mixed-citation xml:lang="en">Stefanska, B., Sroka, J., Katzer, F., Golinski, P., Nowak, W. (2020). The effect of probiotics, phytobiotics and their combination as feed additives in the diet of dairy calves on performance, rumen fermentation and blood metabolites during the preweaning period. Animal Feed Science and Technology, 272, Article 114728. https://doi.org/10.1016/j.anifeedsci.2020.114738</mixed-citation></citation-alternatives></ref><ref id="cit88"><label>88</label><citation-alternatives><mixed-citation xml:lang="ru">Park, T., Yang, C., Yu, Z. (2019). Specific inhibitors of lysozyme and peptidases inhibit the growth of the rumen protozoan Entodinium caudatum without decreasing feed digestion or fermentation in vitro. Journal of Applied Microbiology, 127(3), 670–682. https://doi.org/10.1111/jam.14341</mixed-citation><mixed-citation xml:lang="en">Park, T., Yang, C., Yu, Z. (2019). Specific inhibitors of lysozyme and peptidases inhibit the growth of the rumen protozoan Entodinium caudatum without decreasing feed digestion or fermentation in vitro. Journal of Applied Microbiology, 127(3), 670–682. https://doi.org/10.1111/jam.14341</mixed-citation></citation-alternatives></ref><ref id="cit89"><label>89</label><citation-alternatives><mixed-citation xml:lang="ru">Monteiro, H. F., Zhou, Z., Gomes, M. S., Peixoto, P. M. G., Bonsaglia, E. C. R., Canisso, I. F. et al. (2022). Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows. Scientific Reports, 12(1), Article 4904. https://doi.org/10.1038/s41598-022-08761-5</mixed-citation><mixed-citation xml:lang="en">Monteiro, H. F., Zhou, Z., Gomes, M. S., Peixoto, P. M. G., Bonsaglia, E. C. R., Canisso, I. F. et al. (2022). Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows. Scientific Reports, 12(1), Article 4904. https://doi.org/10.1038/s41598-022-08761-5</mixed-citation></citation-alternatives></ref><ref id="cit90"><label>90</label><citation-alternatives><mixed-citation xml:lang="ru">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(2), 523–536. https://doi.org/10.1007/s00248-018-1234-9</mixed-citation><mixed-citation xml:lang="en">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(2), 523–536. https://doi.org/10.1007/s00248-018-1234-9</mixed-citation></citation-alternatives></ref><ref id="cit91"><label>91</label><citation-alternatives><mixed-citation xml:lang="ru">Snelling, T. J., Auffret, M. D., Duthie, C.-A., Stewart, R. D., Watson, M., Dewhurst, R. J.et al. (2019). Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements. Animal Microbiome, 1(1), Article 16. https://doi.org/10.1186/s42523-019-0018-y</mixed-citation><mixed-citation xml:lang="en">Snelling, T. J., Auffret, M. D., Duthie, C.-A., Stewart, R. D., Watson, M., Dewhurst, R. J.et al. (2019). Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements. Animal Microbiome, 1(1), Article 16. https://doi.org/10.1186/s42523-019-0018-y</mixed-citation></citation-alternatives></ref><ref id="cit92"><label>92</label><citation-alternatives><mixed-citation xml:lang="ru">Loor, J.J., Elolimy, A. A., McCann, J.C. (2016). Dietary impacts on rumen microbiota in beef and dairy production. Animal Frontiers, 6(3), 22–29. https://doi.org/10.2527/af.2016-0030</mixed-citation><mixed-citation xml:lang="en">Loor, J.J., Elolimy, A. A., McCann, J.C. (2016). Dietary impacts on rumen microbiota in beef and dairy production. Animal Frontiers, 6(3), 22–29. https://doi.org/10.2527/af.2016-0030</mixed-citation></citation-alternatives></ref><ref id="cit93"><label>93</label><citation-alternatives><mixed-citation xml:lang="ru">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(14), 4949–4958. https://doi.org/10.1128/AEM.07759-11</mixed-citation><mixed-citation xml:lang="en">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(14), 4949–4958. https://doi.org/10.1128/AEM.07759-11</mixed-citation></citation-alternatives></ref></ref-list><fn-group><fn fn-type="conflict"><p>The authors declare that there are no conflicts of interest present.</p></fn></fn-group></back></article>
