{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T02:32:45Z","timestamp":1793154765505,"version":"4.5.0"},"reference-count":90,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Direct-fed microbials (DFM) have been used to improve livestock production efficiency and reduce environmental impact. Spore-forming bacteria such as Bacillus spp. present handling and processing advantages for use as a DFM; however, more information is needed about their effects in beef cattle. The objective of this study was to evaluate the effect of a DFM composed of a mixture of B. subtilis and B. licheniformis on growth performance, nutrient utilization, enteric methane (CH4) emissions, microbiome of ruminal fluid and feces, and metabolome of plasma and ruminal fluid. Angus crossbred heifers (n\u2009=\u2009108; 318\u2009\u00b1\u200940\u2009kg of body weight) were used in a generalized randomized block design. Heifers were fed a sorghum silage-based diet containing the following treatments: 1) control (CTL, no additive), or 2) Bacillus-based DFM (BOV, 310\u2009mg\/kg of diet dry matter [DM]), to provide an average of 3\u2009g\/animal\/d. No effect of treatment (P\u2009&amp;gt;\u20090.05) was observed for DM intake, average daily gain, or gain-to-feed ratio. The DFM inclusion did not affect (P\u2009&amp;gt;\u20090.05) the apparent total tract digestibility of nutrients or CH4 emissions. Alpha and beta diversity of fecal and ruminal microbiome did not differ with supplementation (P\u2009&amp;gt;\u20090.05). Multivariate analysis indicated minimal impact of the DFM on ruminal and plasma metabolomes. In ruminal fluid, supplementation with the DFM reduced the abundance of three metabolites after false discovery rate (FDR) correction (FDR &amp;lt; 0.05), and pathway analysis indicated that the ubiquinone biosynthesis pathway was enriched by DFM supplementation (P\u2009\u2264\u20090.05). In plasma, two metabolites were differentially abundant between treatments, with proline being more abundant and serine less abundant in heifers supplemented with the DFM than in control heifers (P\u2009\u2264\u20090.05). In summary, supplementation with a Bacillus-based DFM did not affect growth performance, efficiency of feed utilization, nutrient digestibility, or CH4 emissions in beef heifers under the experimental conditions of this trial. Minimal changes were observed in the ruminal and fecal microbiomes and the ruminal and plasma metabolomes, suggesting a limited microbial or systemic impact. Further research is needed to clarify the conditions and mechanisms by which Bacillus-based DFM may exert beneficial effects in beef cattle.<\/jats:p>","DOI":"10.1093\/jas\/skag304","type":"journal-article","created":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T12:27:44Z","timestamp":1790425664000},"source":"Crossref","is-referenced-by-count":0,"title":["Supplementation of a\n                    <i>Bacillus<\/i>\n                    -based DFM mixture on growth performance, methane emissions, microbiome, and metabolome in backgrounding beef heifers"],"prefix":"10.1093","volume":"104","author":[{"given":"Araceli","family":"Maderal","sequence":"first","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignacio","family":"Fernandez-Marenchino","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5563-1956","authenticated-orcid":false,"given":"Federico","family":"Tarnonsky","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7674-3850","authenticated-orcid":false,"given":"Juan","family":"Vargas","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federico","family":"Podversich","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3240-0338","authenticated-orcid":false,"given":"Wilmer","family":"Cuervo","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanesa","family":"Ramirez-Sepulveda","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Horacio","family":"Blanchard","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camila","family":"Gomez-Lopez","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Macarena","family":"Gomez-Salmoral","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8297-7442","authenticated-orcid":false,"given":"Tessa M","family":"Schulmeister","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar Cezar Muller","family":"Queiroz","sequence":"additional","affiliation":[{"name":"Novonesis , Lyngby 2800,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1819-4013","authenticated-orcid":false,"given":"Bruno Ieda","family":"Cappellozza","sequence":"additional","affiliation":[{"name":"Novonesis , Lyngby 2800,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3875-6156","authenticated-orcid":false,"given":"Ibukun","family":"Ogunade","sequence":"additional","affiliation":[{"name":"School of Agriculture and Food Systems, West Virginia University , Morgantown, WV 26506,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5174-3427","authenticated-orcid":false,"given":"Nicolas","family":"DiLorenzo","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Marianna, FL 32446,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"2026102721570535500_skag304-B1","doi-asserted-by":"publisher","first-page":"012050","DOI":"10.1088\/1755-1315\/788\/1\/012050","article-title":"Effects of probiotics and encapsulated probiotics on enteric methane emission and nutrient digestibility in vitro","volume":"788","author":"Abdelbagi","year":"2021","journal-title":"IOP Conf Ser Earth Environ Sci"},{"key":"2026102721570535500_skag304-B2","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.chom.2018.05.003","article-title":"Gut microbiota regulation of tryptophan metabolism in health and disease","volume":"23","author":"Agus","year":"2018","journal-title":"Cell Host Microbe"},{"key":"2026102721570535500_skag304-B3","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1093\/jas\/skae234.587","article-title":"PSV-2 Rumen fluid metabolomics of dairy cows fed combinations of essential oil blend, onion peel extract and prebiotics using the RUSITEC system","volume":"102","author":"Alabi","year":"2024","journal-title":"J Anim Sci"},{"key":"2026102721570535500_skag304-B117920","doi-asserted-by":"publisher","first-page":"G1288","DOI":"10.1152\/ajpgi.00341.2012","article-title":"Critical role of gut microbiota in the production of biologically active, free catecholamines in the gut lumen of mice","volume":"303","year":"2012","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2026102721570535500_skag304-B4","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1017\/S1751731119003100","article-title":"Review: fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation","volume":"14","author":"Beauchemin","year":"2020","journal-title":"Animal"},{"key":"2026102721570535500_skag304-B5","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.2527\/jas1979.4961577x","article-title":"Free amino acids in blood of ruminants\u2014physiological and nutritional regulation","volume":"49","author":"Bergen","year":"1979","journal-title":"J Anim Sci"},{"key":"2026102721570535500_skag304-B6","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":"2026102721570535500_skag304-B7","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1042\/bj1560435","article-title":"Role of ubiquinone in the mitochondrial generation of hydrogen peroxide","volume":"156","author":"Boveris","year":"1976","journal-title":"Biochem J"},{"key":"2026102721570535500_skag304-B8","doi-asserted-by":"publisher","first-page":"748","DOI":"10.4315\/0362-028X-66.5.748","article-title":"Prevalence of Escherichia coli O157: H7 and performance by beef feedlot cattle given Lactobacillus direct-fed microbials","volume":"66","author":"Brashears","year":"2003","journal-title":"J Food Prot"},{"key":"2026102721570535500_skag304-B9","doi-asserted-by":"publisher","first-page":"105068","DOI":"10.1016\/j.livsci.2022.105068","article-title":"Effect of a Bacillus probiotic strain on Nellore cattle finished on pasture during the dry season","volume":"264","author":"Calaca","year":"2022","journal-title":"Livest Sci"},{"key":"2026102721570535500_skag304-B10","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":"2026102721570535500_skag304-B11","doi-asserted-by":"publisher","first-page":"2344","DOI":"10.1128\/AEM.68.5.2344-2352.2002","article-title":"Bacillus probiotics: spore germination in the gastrointestinal tract","volume":"68","author":"Casula","year":"2002","journal-title":"Appl Environ Microbiol"},{"key":"2026102721570535500_skag304-B12","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.3390\/ani11061519","article-title":"Live Bacillus subtilis natto promotes rumen fermentation by modulating rumen microbiota in vitro","volume":"11","author":"Chang","year":"2021","journal-title":"Animals"},{"key":"2026102721570535500_skag304-B13","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3920\/BM2008.1002","article-title":"Probiotics in animal nutrition and health","volume":"1","author":"Chaucheyras-Durand","year":"2010","journal-title":"Benef Microbes"},{"key":"2026102721570535500_skag304-B14","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/s41596-019-0264-1","article-title":"Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data","volume":"15","author":"Chong","year":"2020","journal-title":"Nat Protoc"},{"key":"2026102721570535500_skag304-B15","doi-asserted-by":"publisher","first-page":"302","DOI":"10.15232\/S1080-7446(15)30493-9","article-title":"Effects of concentration and source of wet distillers grains on digestibility of steam-flaked corn-based diets fed to finishing steers","volume":"27","author":"Cole","year":"2011","journal-title":"Prof Anim Sci"},{"key":"2026102721570535500_skag304-B16","doi-asserted-by":"publisher","first-page":"skae259","DOI":"10.1093\/jas\/skae259","article-title":"Effects of a Bacillus-based direct-fed microbial on performance, blood parameters, fecal characteristics, rumen morphometrics, and intestinal gene expression in finishing beef bulls","volume":"102","author":"Cordeiro","year":"2024","journal-title":"J Anim Sci"},{"key":"2026102721570535500_skag304-B17","doi-asserted-by":"publisher","first-page":"76","DOI":"10.15232\/aas.2024-02626","article-title":"Bacillus spp. supplementation stimulates the growth of preweaning bull calves offered milk replacer and pelleted starter supplement","volume":"41","author":"Copani","year":"2025","journal-title":"Appl Anim Sci"},{"key":"2026102721570535500_skag304-B18","doi-asserted-by":"publisher","first-page":"2379","DOI":"10.3390\/ani11082379","article-title":"Effects of Bacillus megatherium 1259 on growth performance, nutrient digestibility, rumen fermentation, and blood biochemical parameters in Holstein bull calves","volume":"11","author":"Deng","year":"2021","journal-title":"Animals"},{"key":"2026102721570535500_skag304-B19","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.anifeedsci.2018.04.014","article-title":"Ruminal fermentation, nutrient metabolism, and methane emissions of sheep in response to dietary supplementation with Bacillus licheniformis","volume":"241","author":"Deng","year":"2018","journal-title":"Anim Feed Sci Technol"},{"key":"2026102721570535500_skag304-B20","doi-asserted-by":"publisher","DOI":"10.1093\/jas\/skac289","article-title":"Effects of feeding different probiotic types on metabolic, performance, and carcass responses of Bos indicus feedlot cattle offered a high-concentrate diet","volume":"100","author":"Dias","year":"2022","journal-title":"J Anim Sci"},{"key":"2026102721570535500_skag304-B21","doi-asserted-by":"publisher","first-page":"259","DOI":"10.22358\/jafs\/66183\/2011","article-title":"Effects of direct-fed microbials and their combinations with yeast culture on in vitro rumen fermentation characteristics","volume":"20","author":"Doto","year":"2011","journal-title":"J Anim Feed Sci"},{"key":"2026102721570535500_skag304-B22","author":"DrugBank"},{"key":"2026102721570535500_skag304-B23","doi-asserted-by":"publisher","first-page":"2006","DOI":"10.3389\/fmicb.2018.02006","article-title":"Probiotic Bacillus amyloliquefaciens C-1 improves growth performance, stimulates GH\/IGF-1, and regulates the gut microbiota of growth-retarded beef calves","volume":"9","author":"Du","year":"2018","journal-title":"Front Microbiol"},{"key":"2026102721570535500_skag304-B24","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.3168\/jds.2023-23831","article-title":"Invited review: \u201cProbiotic\u201d approaches to improving dairy production: reassessing \u201cmagic foo-foo dust","volume":"107","author":"El Jeni","year":"2024","journal-title":"J Dairy Sci"},{"key":"2026102721570535500_skag304-B25","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1017\/S0021859608007752","article-title":"Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle","volume":"146","author":"Ellis","year":"2008","journal-title":"J Agric Sci"},{"key":"2026102721570535500_skag304-B26","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1007\/s12602-018-9492-x","article-title":"Recent advances in the physiology of spore formation for Bacillus probiotic production","volume":"11","author":"Elisashvili","year":"2019","journal-title":"Probiotics Antimicrob Proteins"},{"key":"2026102721570535500_skag304-B27","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.3389\/fmicb.2017.01490","article-title":"Bacillus as potential probiotics: status, concerns, and future perspectives","volume":"8","author":"Elshaghabee","year":"2017","journal-title":"Front Microbiol"},{"key":"2026102721570535500_skag304-B28","doi-asserted-by":"publisher","first-page":"233","DOI":"10.3390\/metabo10060233","article-title":"The bovine metabolome","volume":"10","author":"Foroutan","year":"2020","journal-title":"Metabolites."},{"key":"2026102721570535500_skag304-B29","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.abb.2015.08.012","article-title":"Microbial oxidative stress response: novel insights from environmental facultative anaerobic bacteria","volume":"584","author":"Fu","year":"2015","journal-title":"Arch Biochem Biophys"},{"key":"2026102721570535500_skag304-B30","doi-asserted-by":"crossref","first-page":"281","DOI":"10.19103\/AS.2020.0067.10","volume-title":"Improving rumen function","author":"Gilbert","year":"2020"},{"key":"2026102721570535500_skag304-B31","doi-asserted-by":"publisher","first-page":"476","DOI":"10.3390\/ani15040476","article-title":"In vitro investigation of the effects of Bacillus subtilis-810B and Bacillus licheniformis-809A on rumen fermentation and microbiota","volume":"15","author":"Gresse","year":"2025","journal-title":"Animals"},{"key":"2026102721570535500_skag304-B32","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1071\/AN20295","article-title":"Feed additives as a strategic approach to reduce enteric methane production in cattle: Modes of action, effectiveness, and safety","volume":"62","author":"Honan","year":"2021","journal-title":"Anim Prod Sci"},{"key":"2026102721570535500_skag304-B33","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1016\/j.femsre.2004.12.001","article-title":"The use of bacterial spore formers as probiotics","volume":"29","author":"Hong","year":"2005","journal-title":"FEMS Microbiol Rev"},{"key":"2026102721570535500_skag304-B34","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1007\/978-94-011-5860-2_7","volume-title":"Probiotics 2: Applications and practical aspects","author":"Huber","year":"1997"},{"key":"2026102721570535500_skag304-B35","doi-asserted-by":"publisher","first-page":"skaf135","DOI":"10.1093\/jas\/skaf135","article-title":"Maternal supplementation of a Bacillus-based direct-fed microbials altered the cow prepartum plasma metabolome and the calf plasma metabolome before and after vaccination","volume":"103","author":"Izquierdo","year":"2025","journal-title":"J Anim Sci."},{"key":"2026102721570535500_skag304-B36","doi-asserted-by":"publisher","first-page":"16712","DOI":"10.1038\/s41598-018-35081-4","article-title":"Influence of dietary supplementation with Bacillus licheniformis and Saccharomyces cerevisiae as alternatives to monensin on growth performance, antioxidant, immunity, ruminal fermentation, and microbial diversity of fattening lambs","volume":"8","author":"Jia","year":"2018","journal-title":"Sci Rep"},{"key":"2026102721570535500_skag304-B37","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1021\/es00051a025","article-title":"Measurement of methane emissions from ruminant livestock using a SF6 tracer technique","volume":"28","author":"Johnson","year":"1994","journal-title":"Environ Sci Technol"},{"key":"2026102721570535500_skag304-B38","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1073\/pnas.0507121102","article-title":"The Bacillus subtilis spore coat provides \u201ceat resistance\u201d during phagocytic predation by the protozoan Tetrahymena thermophila","volume":"103","author":"Klobutcher","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026102721570535500_skag304-B39","doi-asserted-by":"publisher","first-page":"514","DOI":"10.5455\/japa.20141028014145","article-title":"Isolation of Enterococcus faecium and Enterococcus cecorum from bovine rumen using modern techniques","volume":"4","author":"Khattab","year":"2014","journal-title":"J Anim Prod Adv"},{"key":"2026102721570535500_skag304-B40","doi-asserted-by":"publisher","first-page":"e13580","DOI":"10.1111\/asj.13580","article-title":"Effect of Bacillus subtilis C-3102 supplementation in milk replacer on growth and rumen microbiota in pre-weaned calves","volume":"92","author":"Koike","year":"2021","journal-title":"Anim Sci J"},{"key":"2026102721570535500_skag304-B41","doi-asserted-by":"publisher","first-page":"399","DOI":"10.22358\/jafs\/66409\/2009","article-title":"Performance of Holstein calves fed milk-replacer and starter mixture supplemented with probiotic feed additive","volume":"18","author":"Kowalski","year":"2009","journal-title":"J Anim Feed Sci"},{"key":"2026102721570535500_skag304-B42","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.3168\/jds.2012-5752","article-title":"Effect of diet composition and incubation time on feed indigestible neutral detergent fiber concentration in dairy cows","volume":"96","author":"Krizsan","year":"2013","journal-title":"J Dairy Sci"},{"key":"2026102721570535500_skag304-B43","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1080\/00071668.2015.1101053","article-title":"Evaluation of a Bacillus direct-fed microbial candidate on digesta viscosity, bacterial translocation, microbiota composition, and bone mineralisation in broiler chickens fed on a rye-based diet","volume":"56","author":"Latorre","year":"2015","journal-title":"Br Poult Sci"},{"key":"2026102721570535500_skag304-B44","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1111\/j.1574-6976.2009.00204.x","article-title":"Indole as an intercellular signal in microbial communities","volume":"34","author":"Lee","year":"2010","journal-title":"FEMS Microbiol Rev"},{"key":"2026102721570535500_skag304-B8849181","doi-asserted-by":"publisher","first-page":"3401","DOI":"10.1021\/ac400099b","article-title":"MyCompoundID: using an evidence-based metabolome library for metabolite identification","volume":"85","author":"Li","year":"2013","journal-title":"Anal Chem"},{"key":"2026102721570535500_skag304-B45","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/s00726-017-2490-6","article-title":"Roles of dietary glycine, proline, and hydroxyproline in collagen synthesis and animal growth","volume":"50","author":"Li","year":"2018","journal-title":"Amino Acids."},{"key":"2026102721570535500_skag304-B46","doi-asserted-by":"publisher","first-page":"skaf093","DOI":"10.1093\/jas\/skaf093","article-title":"Effects of a Bacillus-based direct-fed microbial on digestibility, ruminal in situ nutrient disappearance, microbiome, and fermentation parameters in forage-fed beef cattle","volume":"103","author":"Limede","year":"2025","journal-title":"J Anim Sci"},{"key":"2026102721570535500_skag304-B47","doi-asserted-by":"publisher","first-page":"2927","DOI":"10.3390\/ani13182927","article-title":"The effect of a Bacillus probiotic and essential oils compared to an ionophore on the rumen microbiome composition of feedlot cattle","volume":"13","author":"Linde","year":"2023","journal-title":"Animals"},{"key":"2026102721570535500_skag304-B48","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13099-018-0250-0","article-title":"The role of probiotics, prebiotics and symbiotic in animal nutrition","volume":"10","author":"Markowiak","year":"2018","journal-title":"Gut Pathog"},{"key":"2026102721570535500_skag304-B49","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J"},{"key":"2026102721570535500_skag304-B50","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1111\/j.1574-6968.2001.tb10831.x","article-title":"Ubiquinone biosynthesis in microorganisms","volume":"203","author":"Meganathan","year":"2001","journal-title":"FEMS Microbiol Lett"},{"key":"2026102721570535500_skag304-B51","doi-asserted-by":"publisher","first-page":"txae045","DOI":"10.1093\/tas\/txae045","article-title":"Influence of BOVAMINE DEFEND Plus on growth performance, carcass characteristics, estimated dry matter digestibility, rumen fermentation characteristics, and immune function in finishing beef steers","volume":"8","author":"Miller","year":"2024","journal-title":"Transl Anim Sci"},{"key":"2026102721570535500_skag304-B52","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1111\/jam.13690","article-title":"Bacillus probiotics: an alternative to antibiotics for livestock production","volume":"124","author":"Mingmongkolchai","year":"2018","journal-title":"J Appl Microbiol"},{"key":"2026102721570535500_skag304-B53","doi-asserted-by":"publisher","first-page":"e00673","DOI":"10.1002\/mbo3.673","article-title":"High-production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low-production cattle","volume":"8","author":"Mu","year":"2019","journal-title":"MicrobiologyOpen"},{"key":"2026102721570535500_skag304-B54","doi-asserted-by":"publisher","first-page":"4435","DOI":"10.1021\/acs.analchem.6b03737","article-title":"Development of chemical isotope labeling LC-MS for milk metabolomics: comprehensive and quantitative profiling of the amine\/phenol submetabolome","volume":"89","author":"Mung","year":"2017","journal-title":"Anal Chem"},{"key":"2026102721570535500_skag304-B55","volume-title":"Nutrient requirements of beef cattle","author":"National Academies of Sciences, Engineering, and Medicine (NASEM)","year":"2016"},{"key":"2026102721570535500_skag304-B56","author":"National Cancer Institute"},{"key":"2026102721570535500_skag304-B57","doi-asserted-by":"publisher","DOI":"10.1002\/9783527615353.ch13","volume-title":"Biotechnology in animal feeds and animal feeding","author":"Newbold","year":"1995"},{"key":"2026102721570535500_skag304-B58","doi-asserted-by":"publisher","first-page":"545","DOI":"10.3390\/toxins10120545","article-title":"Biomarker of aflatoxin ingestion: \u00b9H NMR-based plasma metabolomics of dairy cows fed aflatoxin B\u2081 with or without sequestering agents","volume":"10","author":"Ogunade","year":"2018","journal-title":"Toxins (Basel)."},{"key":"2026102721570535500_skag304-B59","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.3168\/jds.2023-23876","article-title":"Effects of direct-fed microbial supplement on ruminal and plasma metabolome of early-lactation dairy cows: untargeted metabolomics approach","volume":"107","author":"Oyebade","year":"2024","journal-title":"J Dairy Sci"},{"key":"2026102721570535500_skag304-B60","doi-asserted-by":"publisher","first-page":"txac067","DOI":"10.1093\/tas\/txac067","article-title":"Effects of a Bacillus-based direct-fed microbial on in vitro nutrient digestibility of forage and high-starch concentrate substrates","volume":"6","author":"Pan","year":"2022","journal-title":"Transl Anim Sci."},{"key":"2026102721570535500_skag304-B7416532","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab382","article-title":"MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights","volume":"49","author":"Pang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026102721570535500_skag304-B61","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.livsci.2014.06.008","article-title":"The beneficial effect of Enterococcus faecium on the in vitro ruminal fermentation rate and extent of three typical total mixed rations in northern China","volume":"167","author":"Pang","year":"2014","journal-title":"Livest Sci"},{"key":"2026102721570535500_skag304-B62","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3168\/jdsc.2024-0566","article-title":"Comparing rumen fluid collection methods on fermentation profile and microbial population in lactating dairy cows","volume":"6","author":"Pathak","year":"2025","journal-title":"JDS Commun"},{"key":"2026102721570535500_skag304-B63","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1111\/j.1439-0396.2011.01173.x","article-title":"Effect of feeding Bacillus subtilis natto fermentation product on milk production and composition, blood metabolites and rumen fermentation in early lactation dairy cows","volume":"96","author":"Peng","year":"2012","journal-title":"J Anim Physiol Anim Nutr"},{"key":"2026102721570535500_skag304-B64","doi-asserted-by":"publisher","first-page":"287","DOI":"10.4315\/0362-028X-70.2.287","article-title":"Effect of Lactobacillus acidophilus strain NP51 on Escherichia coli O157: H7 fecal shedding and finishing performance in beef feedlot cattle","volume":"70","author":"Peterson","year":"2007","journal-title":"J Food Prot"},{"key":"2026102721570535500_skag304-B65","doi-asserted-by":"publisher","first-page":"7661","DOI":"10.3168\/jds.2017-13858","article-title":"Symposium review: understanding diet\u2013microbe interactions to enhance productivity of dairy cows","volume":"101","author":"Pitta","year":"2018","journal-title":"J Dairy Sci"},{"key":"2026102721570535500_skag304-B66","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1111\/j.1439-0396.2009.00926.x","article-title":"Effect of supplemental Bacillus cultures on rumen fermentation and milk yield in Chinese Holstein cows","volume":"94","author":"Qiao","year":"2010","journal-title":"J Anim Physiol Anim Nutr"},{"key":"2026102721570535500_skag304-B67","first-page":"78","article-title":"Addition of a Bacillus-based probiotic to the diet of pre-ruminant calves: Influence on growth, health, and blood parameters","volume":"8","author":"Riddell","year":"2010","journal-title":"Int J Appl Res Vet Med"},{"key":"2026102721570535500_skag304-B68","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1007\/s11259-009-9318-0","article-title":"Administration of Bacillus coagulans in calves: recovery from fecal samples and evaluation of functional aspects of spores","volume":"33","author":"Ripamonti","year":"2009","journal-title":"Vet Res Commun"},{"key":"2026102721570535500_skag304-B69","doi-asserted-by":"publisher","first-page":"txae054","DOI":"10.1093\/tas\/txae054","article-title":"Effects of Bacillus subtilis on in vitro ruminal fermentation and methane production","volume":"8","author":"Sarmikasoglou","year":"2024","journal-title":"Transl Anim Sci"},{"key":"2026102721570535500_skag304-B70","doi-asserted-by":"publisher","first-page":"txab002","DOI":"10.1093\/tas\/txab002","article-title":"Evaluation of Bacillus subtilis PB6 on feedlot phase growth performance, efficiency of dietary net energy utilization, and fecal and subiliac lymph node Salmonella prevalence in spring placement yearling beef steers fed in southeastern South Dakota","volume":"5","author":"Smith","year":"2021","journal-title":"Transl Anim Sci"},{"key":"2026102721570535500_skag304-B71","doi-asserted-by":"publisher","first-page":"txaa163","DOI":"10.1093\/tas\/txaa163","article-title":"Effects of Bacillus subtilis PB6 and\/or chromium propionate supplementation on clinical health, growth performance, and carcass traits of high-risk cattle during the feedlot receiving and finishing periods","volume":"4","author":"Smock","year":"2020","journal-title":"Transl Anim Sci"},{"key":"2026102721570535500_skag304-B72","doi-asserted-by":"publisher","first-page":"txag046","DOI":"10.1093\/tas\/txag046","article-title":"Effects of supplementing a Bacillus-based direct-fed microbial on feed intake, apparent total-tract nutrient digestibility, growth rates, and metabolic responses of Bos indicus beef heifers during the dry and early vegetative seasons","volume":"10","author":"Souza","year":"2026","journal-title":"Transl Anim Sci"},{"key":"2026102721570535500_skag304-B73","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.livsci.2017.03.023","article-title":"Lactation performance and diet digestibility of dairy cows in response to the supplementation of Bacillus subtilis spores","volume":"200","author":"Souza","year":"2017","journal-title":"Livest Sci"},{"key":"2026102721570535500_skag304-B74","doi-asserted-by":"publisher","first-page":"e11151","DOI":"10.7717\/peerj.11151","article-title":"Research progress on the application of feed additives in ruminal methane emission reduction: a review","volume":"9","author":"Sun","year":"2021","journal-title":"PeerJ."},{"key":"2026102721570535500_skag304-B75","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1017\/S1751731112001188","article-title":"Effects of Bacillus subtilis natto on milk production, rumen fermentation and ruminal microbiome of dairy cows","volume":"7","author":"Sun","year":"2013","journal-title":"Animal"},{"key":"2026102721570535500_skag304-B76","doi-asserted-by":"publisher","first-page":"5851","DOI":"10.3168\/jds.2010-3263","article-title":"Effects of Bacillus subtilis natto on performance and immune function of preweaning calves","volume":"93","author":"Sun","year":"2010","journal-title":"J Dairy Sci"},{"key":"2026102721570535500_skag304-B77","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1007\/s00284-016-0986-z","article-title":"Effects of Bacillus subtilis natto and different components in culture on rumen fermentation and rumen functional bacteria in vitro","volume":"72","author":"Sun","year":"2016","journal-title":"Curr. Microbiol"},{"key":"2026102721570535500_skag304-B78","doi-asserted-by":"publisher","first-page":"539","DOI":"10.4315\/0362-028X-71.3.539","article-title":"Comparative effect of direct-fed microbials on fecal shedding of Escherichia coli O157: H7 and Salmonella in naturally infected feedlot cattle","volume":"71","author":"Tabe","year":"2008","journal-title":"J Food Prot"},{"key":"2026102721570535500_skag304-B79","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3389\/fmicb.2015.00037","article-title":"Shifts in metabolic hydrogen sinks in the methanogenesis inhibited ruminal fermentation: a meta-analysis","volume":"6","author":"Ungerfeld","year":"2015","journal-title":"Front Microbiol"},{"key":"2026102721570535500_skag304-B80","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1264\/jsme2.ME14176","article-title":"Effect of probiotics\/prebiotics on cattle health and productivity","volume":"30","author":"Uyeno","year":"2015","journal-title":"Microbes Environ"},{"key":"2026102721570535500_skag304-B81","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":"2026102721570535500_skag304-B26134513","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01682-17","article-title":"Impact of \u201craised without antibiotics\u201d beef cattle production practices on occurrences of antimicrobial resistance","volume":"83.","author":"Vikram","year":"2017","journal-title":"Appl. Environ. Microbiol"},{"key":"2026102721570535500_skag304-B82","doi-asserted-by":"publisher","first-page":"D622","DOI":"10.1093\/nar\/gkab1062","article-title":"HMDB 5.0: The Human Metabolome Database for 2022","volume":"50","author":"Wishart","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026102721570535500_skag304-B83","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.chroma.2015.12.007","article-title":"Sample normalization methods in quantitative metabolomics","volume":"1430","author":"Wu","year":"2016","journal-title":"J Chromatogr A"},{"key":"2026102721570535500_skag304-B84","doi-asserted-by":"publisher","first-page":"553","DOI":"10.5713\/ajas.1995.553","article-title":"Influence of direct-fed microbials on ruminal microbial fermentation and performance of ruminants: a review","volume":"8","author":"Yoon","year":"1995","journal-title":"Asian-Australas J Anim Sci"},{"key":"2026102721570535500_skag304-B85","doi-asserted-by":"publisher","first-page":"12108","DOI":"10.1021\/acs.analchem.9b03431","article-title":"Metabolomic coverage of chemical-group-submetabolome analysis: Group classification and four-channel chemical isotope labeling LC-MS","volume":"91","author":"Zhao","year":"2019","journal-title":"Anal Chem"},{"key":"2026102721570535500_skag304-B86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-030-51652-9_1","volume-title":"Cancer metabolomics. Adv Exp Med Biol","author":"Zhao","year":"2021"}],"container-title":["Journal of Animal Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jas\/advance-article-pdf\/doi\/10.1093\/jas\/skag304\/71402793\/skag304.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skag304\/71402793\/skag304.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skag304\/71402793\/skag304.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T01:57:15Z","timestamp":1793152635000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jas\/article\/doi\/10.1093\/jas\/skag304\/8836610"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":90,"URL":"https:\/\/doi.org\/10.1093\/jas\/skag304","relation":{},"ISSN":["0021-8812","1525-3163"],"issn-type":[{"value":"0021-8812","type":"print"},{"value":"1525-3163","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"skag304"}}