{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T11:23:11Z","timestamp":1783596191221,"version":"3.55.0"},"reference-count":42,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Laboratory of Livestock and Forage Resources Utilization","award":["BSGJSYS202603"],"award-info":[{"award-number":["BSGJSYS202603"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Alterations in microbiota, transcript and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16s rRNA, transcriptome sequencing and liquid chromatography\u2013mass spectrometry to investigate intestinal microbiota, genes and metabolic profiles in the ileum of Hu sheep fed broccoli extract. Here, we randomly allocated 14 Hu sheep to two diets: a basal diet without any supplementation (NC) and a basal diet supplemented with 200 mg\/kg broccoli tail (BT). After 60 days of treatment, blood and jejunal samples were collected for serum biochemical indicators and multi-omics analysis. In this study, the extract of broccoli tails had a significant effect on the serum biochemical indicators, including white blood cells, red blood cells, mean corpuscular volume, mean corpuscular hemoglobin concentration, mean platelet volume, triglycerides and total protein in Hu sheep (p &lt; 0.05). Transcriptomic analysis showed that the 672 differentially expressed genes between the NC and BT groups were primarily enriched in linoleic acid metabolism, steroid hormone biosynthesis, and cholesterol metabolism. Metabolomics analysis using Kyoto Encyclopedia of Genes and Genomes enrichment showed that the 41 differentially abundant metabolites were mainly enriched in bile secretion, vitamin B6 metabolism, and the mTOR signaling pathway. 16S rRNA sequencing results indicated that the extract of broccoli tails increased the relative abundance of Peptostreptococcaceae and decreased the relative abundance of Lachnospiraceae, Lachnospirales, and Bacteroidaceae. Integrated transcriptome, metabolome, and microbiome analysis showed that the gut microbiota and host transcriptomic changes may participate in systemic metabolic regulation by modulating amino acid metabolism, lipid signal transduction, nucleotide metabolism, and vitamin B6-related metabolic pathways. These findings demonstrate that the extract of broccoli tails modulates intestinal gene expression, systemic metabolism, and gut microbial ecology in Hu sheep, providing new insights into the utilization of agricultural byproducts as a functional feed supplement for ruminants.<\/jats:p>","DOI":"10.3390\/vetsci13070663","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T17:27:31Z","timestamp":1783531651000},"page":"663","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Conjoint Analysis of Sheep Microbiome, Metabolome, and Transcriptome Revealed the Effect Mechanisms of Feeding with Broccoli Extract"],"prefix":"10.3390","volume":"13","author":[{"given":"Gang","family":"Zhou","sequence":"first","affiliation":[{"name":"College of Life Science and Technology, Tarim University, Alar 843300, China"},{"name":"Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar 843300, China"},{"name":"Huaiyin Institute of Agricultural Sciences in Xuhuai Regio, Huaian 223000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Huaiyin Normal University, Huai\u2019an 223300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuanxuan","family":"Pu","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Livestock and Grass Resources Utilization around Tarim, Ministry of Agriculture and Rural Areas (Co-Construction by Ministries and Provinces), Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiugui","family":"Ning","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoshan","family":"Guo","sequence":"additional","affiliation":[{"name":"Huaiyin Institute of Agricultural Sciences in Xuhuai Regio, Huaian 223000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liwei","family":"Wang","sequence":"additional","affiliation":[{"name":"Huaiyin Institute of Agricultural Sciences in Xuhuai Regio, Huaian 223000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhong","family":"Zhong","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guolian","family":"Wang","sequence":"additional","affiliation":[{"name":"Huaiyin Institute of Agricultural Sciences in Xuhuai Regio, Huaian 223000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3909-7869","authenticated-orcid":false,"given":"Xuefeng","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Livestock and Grass Resources Utilization around Tarim, Ministry of Agriculture and Rural Areas (Co-Construction by Ministries and Provinces), Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengzhi","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"s31","DOI":"10.1017\/S175173111700324X","article-title":"Review: Feed demand landscape and implications of food-not feed strategy for food security and climate change","volume":"12","author":"Makkar","year":"2018","journal-title":"Animal"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.ifset.2011.04.005","article-title":"Composition and antioxidant capacity of a novel beverage produced with green tea and minimally processed byproducts of broccoli","volume":"12","author":"Moreno","year":"2011","journal-title":"Innov. Food Sci. Emerg. Technol."},{"key":"ref_3","first-page":"220","article-title":"Anticancer activity of broccoli, its organosulfur and polyphenolic compounds","volume":"489","author":"Gasmi","year":"2024","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Yan, L., Zhou, G., Shahzad, K., Zhang, H., Yu, X., Wang, Y., Yang, N., Wang, M., and Zhang, X. (2023). Research progress on utilization technology of broccoli stalk. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1138700"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1089\/jmf.2018.0024","article-title":"Isothiocyanate from broccoli, sulforaphane, and its properties","volume":"22","author":"Vanduchova","year":"2019","journal-title":"J. Med. Food"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Patra, A.K. (2012). An overview of antimicrobial properties of different classes of phytochemicals. Dietary Phytochemicals and Microbes, Springer.","DOI":"10.1007\/978-94-007-3926-0"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"txaa078","DOI":"10.1093\/tas\/txaa078","article-title":"Broccoli byproduct-wheat straw silage as a feed resource for fattening lambs","volume":"4","author":"Partovi","year":"2020","journal-title":"Transl. Anim. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"101530","DOI":"10.1016\/j.animal.2025.101530","article-title":"Feeding broccoli and cauliflower to dairy sheep: Influence on feed intake, metabolic health status and milk production and composition","volume":"19","author":"Martin","year":"2025","journal-title":"Animal"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Chen, S., Zhang, X., Zhu, T., Tang, D., Wen, M., Tang, C., Hou, L., Zeng, Z., Tong, S., and Li, X. (2025). Effect of broccoli extract supplement on carcass traits and lipid metabolism in Holstein steers. Front. Genet., 16.","DOI":"10.3389\/fgene.2025.1618682"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"14567","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":"ref_11","doi-asserted-by":"crossref","first-page":"101550","DOI":"10.1016\/j.animal.2025.101550","article-title":"Mucosal barrier function and microbial community of small intestines in sheep in response to dietary energy concentrations","volume":"19","author":"Wang","year":"2025","journal-title":"Animal"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"174539","DOI":"10.1016\/j.scitotenv.2024.174539","article-title":"Aflatoxin B1 as a complicit in intestinal damage caused by Eimeria ovinoidalis in lambs: Novel insights to reveal parasite-gut battle","volume":"947","author":"Chen","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_13","first-page":"41","article-title":"Advancing functional and translational microbiome research through meta-omics","volume":"11","author":"Zhang","year":"2019","journal-title":"Genome Med."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s40104-025-01259-w","article-title":"Multi-omics analysis reveals host-microbe interactions driving divergent energy allocation strategies in Tibetan sheep under cold-season feeding regimes","volume":"16","author":"Wang","year":"2025","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Wang, M., Yi, M., Wang, L., Sun, S., Ling, Y., Zhang, Z., and Cao, H. (2024). Multi-omics analysis reveals the regulatory mechanism of dietary probiotics on the growth performance of fattening sheep. Animals, 14.","DOI":"10.3390\/ani14091285"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Chen, W., Lv, X., Cao, X., Yuan, Z., Wang, S., Getachew, T., Mwacharo, J.M., Haile, A., Al-Samarai, K., and Luo, Y. (2023). Integration of the microbiome, metabolome and transcriptome reveals the interplay between intestinal genes, metabolites and bacteria in E. coli F17-infected sheep. Animals, 13.","DOI":"10.3390\/ani13061050"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Zhang, L., An, X., Xu, Z., Niu, C., Geng, Z., Zhang, J., Shi, H., Chen, Z., Zhang, R., and Yue, Y. (2025). Transcriptome-metabolome analysis reveals that crossbreeding improves meat quality in Hu sheep and their F1-generation sheep. Foods, 14.","DOI":"10.3390\/foods14081384"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"ClusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"W388","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":"ref_20","doi-asserted-by":"crossref","first-page":"e246","DOI":"10.1002\/imt2.246","article-title":"MetOrigin 2.0: Advancing the discovery of microbial metabolites and their origins","volume":"3","author":"Yu","year":"2024","journal-title":"iMeta"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","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":"ref_23","doi-asserted-by":"crossref","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":"ref_24","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Rohart, F., Gautier, B., Singh, A., and Le Cao, K.A. (2017). MixOmics: An R package for \u2019omics feature selection and multiple data integration. PLoS Comput. Biol., 13.","DOI":"10.1101\/108597"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Le Cao, K.A., Boitard, S., and Besse, P. (2011). Sparse PLS discriminant analysis: Biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-253"},{"key":"ref_27","unstructured":"Radostits, O.M., Gay, C.C., Blood, D.C., and Hinch-cliff, K.W. (2000). Veterinary Medicine, W.B. Saunders. [9th ed.]."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4302","DOI":"10.2527\/jas2017.1804","article-title":"Beef steers with average dry matter intake and divergent average daily gain have altered gene expression in the jejunum","volume":"95","author":"Foote","year":"2017","journal-title":"J. Anim. Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s11033-025-10358-w","article-title":"Protective role of sulforaphane in lipid metabolism-related diseases","volume":"52","author":"Zhao","year":"2025","journal-title":"Mol. Biol. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"15126","DOI":"10.1021\/acs.jafc.2c06311","article-title":"Sulforaphane ameliorates hepatic lipid metabolism via modulating lipophagy in vivo and in vitro","volume":"70","author":"Lei","year":"2022","journal-title":"J. Agric. Food Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e1800795","DOI":"10.1002\/mnfr.201800795","article-title":"Sulforaphane improves lipid metabolism by enhancing mitochondrial function and biogenesis in vivo and in vitro","volume":"63","author":"Lei","year":"2019","journal-title":"Mol. Nutr. Food Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1097\/MOG.0000000000000156","article-title":"Bile acids as metabolic regulators","volume":"31","author":"Li","year":"2015","journal-title":"Curr. Opin. Gastroenterol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.cmet.2016.05.005","article-title":"Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism","volume":"24","author":"Wahlstrom","year":"2016","journal-title":"Cell Metab."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Parra, M., Stahl, S., and Hellmann, H. (2018). Vitamin B6 and its role in cell metabolism and physiology. Cells, 7.","DOI":"10.3390\/cells7070084"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.cell.2017.03.035","article-title":"MTOR signaling in growth, metabolism, and disease","volume":"169","author":"Saxton","year":"2017","journal-title":"Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"Lozupone","year":"2012","journal-title":"Nature"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s40168-020-00819-8","article-title":"Multi-omics reveals that the rumen microbiome and its metabolome together modulate host metabolism","volume":"8","author":"Xue","year":"2020","journal-title":"Microbiome"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1111\/jam.14468","article-title":"The composition and stability of the faecal microbiota of Merino sheep","volume":"128","author":"Mamun","year":"2020","journal-title":"J. Appl. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1757-4749-5-23","article-title":"Commensal Clostridia: Leading players in the maintenance of gut homeostasis","volume":"5","author":"Lopetuso","year":"2013","journal-title":"Gut Pathog."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"627","DOI":"10.3390\/d5030627","article-title":"Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities","volume":"5","author":"Biddle","year":"2013","journal-title":"Diversity"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/j.molmed.2012.07.009","article-title":"The endocannabinoid system in inflammatory bowel diseases: From pathophysiology to therapeutic opportunity","volume":"18","author":"Alhouayek","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1016\/j.tim.2016.02.002","article-title":"Functional redundancy-induced stability of gut microbiota subjected to disturbance","volume":"24","author":"Moya","year":"2016","journal-title":"Trends Microbiol."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/7\/663\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T10:44:51Z","timestamp":1783593891000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/7\/663"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,8]]},"references-count":42,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["vetsci13070663"],"URL":"https:\/\/doi.org\/10.3390\/vetsci13070663","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,8]]}}}