Analysis of microorganisms of rotting rose hips by high-throughput sequencing and MALDI-TOF-MS

Rose hips (Rosa rugosa), a rich source of bioactive compounds such as phenols, carotenoids, and vitamins, are increasingly recognized for their nutritional and medicinal value. However, the high nutrient content and moisture levels in fresh rose hips make them highly susceptible to microbial spoilage, which significantly reduces their shelf life and increases food waste. Despite the importance of understanding the microbial communities responsible for spoilage, limited research has focused on this aspect of rose hip preservation. This study aims to bridge this gap by investigating the microbial communities involved in the spoilage of four varieties of Rosa rugosa from Pingyin, Shandong Province, using high-throughput sequencing, MALDI-TOF-MS, and gas chromatography-mass spectrometry (GC-MS) for microbial and volatile organic compound analysis. High- throughput sequencing of 16S rRNA and ITS genes identified a diverse microbial community consisting of both bacteria and fungi, including spoilage-associated species such as Bacillus, Pantoea, Rahnella, Alternaria, and Aspergillus. MALDI-TOF-MS further confirmed these findings, revealing a broader range of microbial species. GC-MS analysis of volatile organic compounds (VOCs) identified key spoilage-related compounds, such as alcohols, ketones, and esters, with correlations between specific VOCs and microbial populations. This study provides valuable insights into the microbial dynamics of rose hip spoilage and offers potential markers for spoilage detection. The integration of high-throughput sequencing, MALDI-TOF-MS, and GC-MS sets a new benchmark for food preservation research, enhancing our ability to monitor and control microbial contamination in fresh fruits.