{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T01:45:59Z","timestamp":1782438359727,"version":"3.54.5"},"reference-count":44,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T00:00:00Z","timestamp":1781913600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"earmarked fund for Inner Mongolia Agriculture and Animal Husbandry Research System","award":["IMAHRS-9"],"award-info":[{"award-number":["IMAHRS-9"]}]},{"name":"2023 National Center of Pratacultural Technology Innovation (under preparation) Major Innovation Platform Construction Project","award":["CCPTZX2023B07"],"award-info":[{"award-number":["CCPTZX2023B07"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Oat (Avena sativa L.) silage fermentation often fails due to insufficient lactic acid bacteria (LAB) and low water-soluble carbohydrate content. We investigated the effects of Compound Radix Pulsatillae (CRP; 40 g\/kg FM) alone or combined with a commercial LAB inoculant (containing L. plantarum, L. buchneri, and Enterococcus faecium, CRP_LA) on oat silage after 60 days. Compared to control (CK), both CRP and CRP_LA increased dry matter and water-soluble carbohydrate retention while reducing fiber components and ammonia nitrogen (p &lt; 0.05). CRP_LA exhibited superior fermentation quality (lowest pH 4.82, highest lactic acid 47.83 g\/kg DM). Using 16S rRNA sequencing and UPLC-MS\/MS metabolomics integrated with weighted gene co-expression network analysis (WGCNA), we identified a brown module strongly associated with CRP_LA treatment. Six hub metabolites, belonging to flavonoids, terpenoids, alkaloids, phenolic acids, and nucleotide derivatives, were significantly elevated in CRP_LA silage and showed strong correlations with Lactobacillus abundance and fermentation quality parameters. Correlation-based network analysis revealed that these hub metabolites positively correlated with Lactobacillus abundance, lactic acid, and water-soluble carbohydrate retention, while negatively correlating with spoilage microorganisms (Enterobacter, Acinetobacter, Leuconostoc) and ammonia nitrogen. This multi-omics study provides a metabolite-centric molecular map of the silage microecosystem reshaped by CRP and LAB co-fermentation. The identified hub metabolites\u2014with predicted antimicrobial, antioxidant, and plant-protective functions\u2014represent potential quality markers for functional silage additive development. Mechanistic validation via targeted metabolite supplementation or pathway-specific gene expression analysis is warranted in future studies.<\/jats:p>","DOI":"10.3390\/ijms27125577","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:09:17Z","timestamp":1782270557000},"page":"5577","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi Omics Analysis Reveals That Compound Radix Pulsatillae and Lactic Acid Bacteria Reprogram the Microbiome Metabolome Network in Oat Silage"],"prefix":"10.3390","volume":"27","author":[{"given":"Yuanyuan","family":"Jing","sequence":"first","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoran","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Qu","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guolin","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhennan","family":"He","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-2639-2263","authenticated-orcid":false,"given":"Siyi","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, No. 22 Zhaojun Road, Yuquan District, Hohhot 010031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengqin","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Grassland Research, Chinese Academy of Agricultural Sciences, No. 120, East Ulanqab Street, Saihan District, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"138800","DOI":"10.1016\/j.ijbiomac.2024.138864","article-title":"Novel strategy to understand the bacteria-enzyme synergy action regulates the ensiling performance of wheat straw silage by multi-omics analysis","volume":"289","author":"Du","year":"2025","journal-title":"Int. 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