Cold-resistant lactic acid bacteria in Jerusalem artichoke silage: quality, microbiome and metabolome dynamics during aerobic exposure on the Qinghai-Tibet Plateau

Forage scarcity during the cold season poses a major challenge to livestock farming on the Qinghai-Tibet Plateau. Jerusalem artichoke (<i>Helianthus tuberosus</i>) offers a promising alternative, but aerobic exposure of its silage leads to nutrient loss and microbial spoilage under low temperatures. This study aimed to evaluate the effects of inoculating cold-resistant lactic acid bacteria (LAB)-<i>Lactiplantibacillus plantarum</i> GN02 (homofermentative) and <i>Levilactobacillus brevis</i> XN25 (heterofermentative)-on silage quality, microbiome, and metabolome dynamics during aerobic exposure. Silage was prepared from Jerusalem artichoke stems and leaves, treated with sterile water (CK), <i>Lpl. plantarum</i> (YZ), <i>Lv. brevis</i> (YD), or their mixture (YZD), and ensiled for 60 days at -5 to 8 °C. Samples were analyzed at 0, 7, and 14 days of aerobic exposure (-10 to 5 °C) for fermentation parameters (pH, organic acids, dry matter, water-soluble carbohydrates, crude protein, fibers), microbial communities via 16S rRNA and ITS sequencing, and metabolites using LC-MS-based untargeted metabolomics. Inoculation with <i>Lpl. plantarum</i> maintained lower pH (<5), higher lactic acid, dry matter, and water-soluble carbohydrates, while suppressing spoilage bacteria (e.g., <i>Carnobacterium</i>, <i>Citrobacter</i>) and enriching <i>Lactobacillus</i>. Metabolomics revealed upregulated flavonoids and octadecanoids, enhancing antioxidant defenses and downregulating carbohydrate degradation pathways. <i>Lv. brevis</i> accelerated spoilage with elevated pH and nutrient loss, whereas the mixture showed intermediate effects. These findings demonstrate <i>Lpl. plantarum</i>'s efficacy in mitigating aerobic deterioration, providing a theoretical basis for optimizing silage preservation and supporting sustainable livestock production in high-altitude regions.