As a globally distributed cereal, wheat is an essential part of the daily human dietary structure. Various changes in nutrient composition and starch structure can reflect the quality of wheat. In this study, we carried out a series of measurements to reveal the levels of wheat quality during long-term storage. We found that the deterioration of wheat was apparent after two years of storage: (1) the content of fatty acid increased from 12.47% to 29.02%; (2) the malondialdehyde content increased to 37.46%; (3) the conductivity significantly increased from 35.71% to 46.79%; and (4) other indexes, such as the amylopectin content, peak viscosity, and disintegration rate, increased noticeably during storage. Moreover, SEM images revealed a certain degree of damage on the surface of starch granules, and an X-ray diffraction (XRD) analysis showed A-type crystalline starch of wheat. Additionally, FTIR spectra suggested that the ratio of amylose and amylopectin decreased with a decreasing content of amylose and increasing content of amylopectin. The ratio of amylose and amylopectin can lead to variations in wheat machining characteristics. Therefore, wheat should be kept at an average of 20 °C with safe water content for less than two years to maintain reasonable quality.

Different storage conditions can influence microbial community structure and metabolic functions, affecting rice grains’ quality. However, the microbiological mechanisms by which different storage conditions affect the quality of rice grains are not yet well understood. This study monitored the quality (the content of starch, protein, etc.) and microbial community structure of rice grains stored under different storage conditions with nitrogen gas atmosphere (RA: normal temperature, horizontal ventilation, RB: normal temperature, vertical ventilation, RC: quasi-low temperature, horizontal ventilation). The results revealed that the rice grains stored under condition RB exhibited significantly lower quality compared to condition RA and RC. In addition, under this condition, the highest relative abundance of Aspergillus (16.0%) and Penicillium (0.4%) and the highest levels of aflatoxin A (3.77 ± 0.07 μg/kg) and ochratoxin B1 (3.19 ± 0.05 μg/kg) were detected, which suggested a higher risk of fungal toxin contamination. Finally, co-occurrence network analysis was performed, and the results revealed that butyl 1,2-benzenedicarboxylate was negatively correlated (p < 0.05) with Moesziomyces and Alternaria. These findings will contribute to the knowledge base of rice storage management and guide the development of effective control measures against undesirable microbial activities.