{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T15:02:47Z","timestamp":1789743767221,"version":"4.0.1"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007823","name":"Alltech","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007823","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiomes"],"abstract":"<jats:p>\n                    Dairy cattle are typically fed a total mixed ration (TMR), which is prepared in an automated mixer wagon. On-farm, effective TMR mixing can often be neglected due to lack of time or training. This leads to a disbalance of intake and potentially detrimental effects on health and production. Using dietary treatments to simulate this effect, this study determined the response of rumen metabolism and microbiome to different concentrate allocations in combination with a live\n                    <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n                    supplement (yeast supplementation, YS). The 4 \u00d7 4 Latin square design consisted of four dairy cows fitted with permanent rumen cannulae, which were fed a partial mixed ration with dietary concentrates (4 kg per cow per day) in an even or an uneven pattern of allocation (concentrate allocation, CA). YS was included in the TMR at a rate of 1 g per cow per day. Rumen metabolism was determined by measuring the pH, volatile fatty acids (VFAs), and ammonia nitrogen (NH\n                    <jats:sub>3<\/jats:sub>\n                    \u2013N). The rumen microbial community was characterised using 16S rRNA gene amplicon sequencing. Both CA and YS had no effect (\n                    <jats:italic>p<\/jats:italic>\n                    &amp;gt; 0.05) on the dry matter intake, milk yield, or composition. CA did not affect the rumen NH\n                    <jats:sub>3<\/jats:sub>\n                    \u2013N and VFA concentrations (\n                    <jats:italic>p<\/jats:italic>\n                    &amp;gt; 0.05). YS inclusion tended to increase the rumen pH (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.088), acetate (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.076), and valerate (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.091). YS significantly increased the total VFA (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.033) and propionate concentrations (\n                    <jats:italic>p<\/jats:italic>\n                    &amp;lt; 0.016). CA had little overall effect on the rumen microbiome beta diversity. However, there was a reduction in the relative abundance of a Prevotellaceae feature associated with an uneven pattern of CA. Bray\u2013Curtis clustering of the microbiome was observed with YS (\n                    <jats:italic>p<\/jats:italic>\n                    = 0.002), driven by a decrease of Gammaproteobacteria and Prevotellaceae features and an increase of a Christensenellaceae feature (LDA &amp;gt; 2.0).\n                  <\/jats:p>","DOI":"10.3389\/frmbi.2026.1884444","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T05:28:23Z","timestamp":1786080503000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Modulation of the rumen microbiome and metabolism in dairy cows by altering the concentrate feeding pattern and the inclusion of Saccharomyces cerevisiae yeast"],"prefix":"10.3389","volume":"5","author":[{"given":"Timothy J.","family":"Snelling","sequence":"first","affiliation":[{"name":"Animal Science Research Centre, Harper Adams University","place":["Edgmond, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine A.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Animal Science Research Centre, Harper Adams University","place":["Edgmond, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen E.","family":"Warren","sequence":"additional","affiliation":[{"name":"Alltech Bioscience Centre","place":["Dunboyne, Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jules","family":"Taylor-Pickard","sequence":"additional","affiliation":[{"name":"Alltech Bioscience Centre","place":["Dunboyne, Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A.","family":"Huntington","sequence":"additional","affiliation":[{"name":"Animal Science Research Centre, Harper Adams University","place":["Edgmond, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam A.","family":"Sinclair","sequence":"additional","affiliation":[{"name":"Animal Science Research Centre, Harper Adams University","place":["Edgmond, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.anifeedsci.2022.115240","article-title":"Association between yeast product feeding and milk production of lactating dairy cows: Multilevel meta-analysis and meta-regression","volume":"285","author":"Abdelli","year":"2022","journal-title":"Anim. Feed Sci. Technol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"4211","DOI":"10.3168\/jds.2009-2977","article-title":"Effect of dietary concentrate on rumen fermentation, digestibility, and nitrogen losses in dairy cows","volume":"93","author":"Agle","year":"2010","journal-title":"J. Dairy Sci."},{"key":"B3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"7751","DOI":"10.3168\/jds.2014-8212","article-title":"Active dry Saccharomyces cerevisiae can alleviate the effect of subacute ruminal acidosis in lactating dairy cows","volume":"97","author":"AlZahal","year":"2014","journal-title":"J. Dairy Sci."},{"key":"B5","volume-title":"Official Methods of Analysis of Association of Official Analytical Chemists","year":"2012"},{"key":"B6","doi-asserted-by":"publisher","first-page":"115476","DOI":"10.1016\/j.anifeedsci.2022.115476","article-title":"The effects of dietary yeast and yeast-derived extracts on rumen microbiota and their function","volume":"294","author":"Baker","year":"2022","journal-title":"Anim. Feed Sci. Technol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1684","DOI":"10.3945\/jn.112.159574","article-title":"Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation","volume":"142","author":"Belanche","year":"2012","journal-title":"J. Nutr."},{"key":"B8","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B10","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1111\/jam.13005","article-title":"Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi","volume":"120","author":"Chaucheyras-Durand","year":"2016","journal-title":"J. Appl. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/j.anifeedsci.2007.04.019","article-title":"Effects of active dry yeasts on the rumen microbial ecosystem: Past, present and future","volume":"145","author":"Chaucheyras-Durand","year":"2008","journal-title":"Anim. Feed Sci. Technol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"5805","DOI":"10.3168\/jds.2022-22860","article-title":"Influence of the concentrate inclusion level in a grass silage\u2013based diet on hepatic transcriptomic profiles in Holstein-Friesian dairy cows in early lactation","volume":"106","author":"Cheng","year":"2023","journal-title":"J. Dairy Sci."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.3168\/jds.2008-1414","article-title":"Meta-analysis of the influence of Saccharomyces cerevisiae supplementation on ruminal parameters and milk production of ruminants","volume":"92","author":"Desnoyers","year":"2009","journal-title":"J. Dairy Sci."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4652","article-title":"Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences","volume":"6","author":"Edgar","year":"2018","journal-title":"PeerJ"},{"key":"B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","article-title":"Conservation evaluation and phylogenetic diversity","volume":"61","author":"Faith","year":"1992","journal-title":"Biol. Conserv."},{"key":"B16","first-page":"1149","article-title":"Statistical power analyses using G*Power 3.1: Tests for correlation and regression analyses","volume-title":"Behavior Research Methods","author":"Faul","year":"2009"},{"key":"B17","doi-asserted-by":"publisher","first-page":"2695","DOI":"10.3168\/jds.s0022-0302(94)77212-x","article-title":"Principal descriptors of body condition score in Holstein cows","volume":"77","author":"Ferguson","year":"1994","journal-title":"J. Dairy Sci."},{"key":"B18","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1038\/s41564-022-01094-z","article-title":"Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis","volume":"7","author":"Forster","year":"2022","journal-title":"Nat. Microbiol"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/srep14567","article-title":"Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range","volume":"5","author":"Henderson","year":"2015","journal-title":"Sci. Rep."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1101\/2024.06.20.599854","article-title":"Broad diversity of human gut bacteria accessible via a traceable strain deposition system","author":"Hitch","year":"2024","journal-title":"bioRxiv"},{"key":"B21","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s40168-024-01760-w","article-title":"Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant","volume":"12","author":"Jin","year":"2024","journal-title":"Microbiome"},{"key":"B22","doi-asserted-by":"publisher","first-page":"100967","DOI":"10.1016\/j.animal.2023.100967","article-title":"Effect of feeding Yucca schidigera extract and a live yeast on the rumen microbiome and performance of dairy cows fed a diet excess in rumen degradable nitrogen","volume":"17","author":"Johnson","year":"2023","journal-title":"Animal"},{"key":"B23","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"3514","DOI":"10.1038\/s41467-020-17041-7","article-title":"Analysis of compositions of microbiomes with bias correction","volume":"11","author":"Lin","year":"2020","journal-title":"Nat. Commun."},{"key":"B25","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1136\/vr.104781","article-title":"Comparison of total\u2010mixed\u2010ration and feed\u2010to\u2010yield strategies on blood profiles and dairy cow health","volume":"183","author":"Little","year":"2018","journal-title":"Vet. Rec."},{"key":"B26","doi-asserted-by":"publisher","first-page":"4360","DOI":"10.3168\/jds.2015-10441","article-title":"A comparison of individual cow versus group concentrate allocation strategies on dry matter intake, milk production, tissue changes, and fertility of Holstein-Friesian cows offered a grass silage diet","volume":"99","author":"Little","year":"2016","journal-title":"J. Dairy Sci."},{"key":"B27","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1186\/s40168-024-01946-2","article-title":"Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites","volume":"12","author":"Luan","year":"2024","journal-title":"Microbiome"},{"key":"B28","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1038\/s41385-018-0087-3","article-title":"Succinate receptor mediates intestinal inflammation and fibrosis","volume":"12","author":"Macias-Ceja","year":"2019","journal-title":"Mucosal Immunol."},{"key":"B29","volume-title":"The Analysis of Agricultural Materials","year":"1986"},{"key":"B30","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1128\/aem.55.6.1570-1573.1989","article-title":"Metabolism and some characteristics of ruminal strains of Megasphaera elsdenii","volume":"55","author":"Marounek","year":"1989","journal-title":"Appl. Environ. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1079\/BJN19960029","article-title":"Mode of action of the yeast Saccharomyces cerevisiae as a feed additive for ruminants","volume":"76","author":"Newbold","year":"1996","journal-title":"Br. J. Nutr."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1099\/ijs.0.63388-0","article-title":"Treponema berlinense sp. nov. and Treponema porcinum sp. nov. novel spirochaetes isolated from porcine faeces","volume":"55","author":"Nordhoff","year":"2005","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0182271","article-title":"Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling","volume":"12","author":"Petri","year":"2017","journal-title":"PloS One"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0083424","article-title":"Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge","volume":"8","author":"Petri","year":"2013","journal-title":"PloS One"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0067824","article-title":"The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle","volume":"8","author":"Pinloche","year":"2013","journal-title":"PloS One"},{"key":"B36","doi-asserted-by":"publisher","first-page":"726","DOI":"10.2527\/jas.2015-9605","article-title":"Transient feeding of a concentrate-rich diet increases the severity of subacute ruminal acidosis in dairy cattle","volume":"94","author":"Pourazad","year":"2016","journal-title":"J. Anim. Sci."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2811","DOI":"10.3168\/jds.2015-9988","article-title":"Effect of concentrate feeding method on the performance of dairy cows in early to mid lactation","volume":"99","author":"Purcell","year":"2016","journal-title":"J. Dairy Sci."},{"key":"B38","doi-asserted-by":"publisher","first-page":"5659","DOI":"10.3168\/jds.2009-2273","article-title":"Influence of detachment procedure and diet on recovery of solid-associated bacteria from sheep ruminal digesta and representativeness of bacterial isolates as assessed by automated ribosomal intergenic spacer analysis-polymerase chain reaction","volume":"92","author":"Ramos","year":"2009","journal-title":"J. Dairy Sci."},{"key":"B39","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.2527\/2003.8151332x","article-title":"Synchrony of nutrient supply to the rumen and dietary energy source and their effects on the growth and metabolism of lambs","volume":"81","author":"Richardson","year":"2003","journal-title":"J. Anim. Sci"},{"key":"B40","doi-asserted-by":"publisher","first-page":"10143","DOI":"10.3168\/jds.2017-12967","article-title":"A 100-Year Review: Total mixed ration feeding of dairy cows","volume":"100","author":"Schingoethe","year":"2017","journal-title":"J. Dairy Sci."},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nbt.4110","article-title":"Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection","volume":"36","author":"Seshadri","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s42523-019-0018-y","article-title":"Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements","volume":"1","author":"Snelling","year":"2019","journal-title":"Anim. Microbiome"},{"key":"B44","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/s41467-018-03317-6","article-title":"Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen","volume":"9","author":"Stewart","year":"2018","journal-title":"Nat. Commun."},{"key":"B45","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1007\/s12223-012-0140-7","article-title":"Variability of Actinobacteria, a minor component of rumen microflora","volume":"57","author":"Su\u013e\u00e1k","year":"2012","journal-title":"Folia Microbiol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"115151","DOI":"10.1016\/j.anifeedsci.2021.115151","article-title":"Milk production, rumen function, and digestion in dairy cows fed diets differing in predominant forage and concentrate type","volume":"248","author":"Tayyab","year":"2022","journal-title":"Anim. Feed Sci. Technol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1017\/S1751731118001568","article-title":"Grass silage particle size when fed with or without maize silage alters performance, reticular pH and metabolism of Holstein-Friesian dairy cows","volume":"13","author":"Tayyab","year":"2019","journal-title":"Animal"},{"key":"B48","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.livsci.2018.09.018","article-title":"Particle size distribution of forages and mixed rations, and their relationship with ration variability and performance of UK dairy herds","volume":"217","author":"Tayyab","year":"2018","journal-title":"Livest. Sci."},{"key":"B49","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature24621","article-title":"A communal catalogue reveals Earth's multiscale microbial diversity","volume":"551","author":"Thompson","year":"2017","journal-title":"Nature"},{"key":"B50","doi-asserted-by":"publisher","first-page":"3583","DOI":"10.3168\/jds.S0022-0302(91)78551-2","article-title":"Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition","volume":"74","author":"Van Soest","year":"1991","journal-title":"J. Dairy Sci."},{"key":"B51","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/s12915-019-0699-4","article-title":"The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health","volume":"17","author":"Waters","year":"2019","journal-title":"BMC Biol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"D643","DOI":"10.1093\/nar\/gkt1209","article-title":"The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks","volume":"42","author":"Yilmaz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B53","doi-asserted-by":"publisher","first-page":"808","DOI":"10.2144\/04365st04","article-title":"Improved extraction of PCR-quality community DNA from digesta and fecal samples","volume":"36","author":"Yu","year":"2004","journal-title":"Biotechniques"},{"key":"B54","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.3168\/jds.2011-4421","article-title":"Review: role of physically effective fiber and estimation of dietary fiber adequacy in high-producing dairy cattle","volume":"95","author":"Zebeli","year":"2012","journal-title":"J. Dairy Sci."},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1016\/j.anifeedsci.2020.114619","article-title":"Effect of high-concentrate diets on microbial composition, function, and the VFAs formation process in the rumen of dairy cows","volume":"269","author":"Zhang","year":"2020","journal-title":"Anim. Feed Sci. Technol."}],"updated-by":[{"DOI":"10.3389\/frmbi.2026.1965017","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000}}],"container-title":["Frontiers in Microbiomes"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frmbi.2026.1884444\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T14:05:52Z","timestamp":1789740352000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frmbi.2026.1884444\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,7]]},"references-count":55,"alternative-id":["10.3389\/frmbi.2026.1884444"],"URL":"https:\/\/doi.org\/10.3389\/frmbi.2026.1884444","relation":{},"ISSN":["2813-4338"],"issn-type":[{"value":"2813-4338","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,7]]},"article-number":"1884444"}}