The shelf life, storage stability and microbial changes of instant rice noodles (IRN) during storage were systematically investigated. The total aerobic viable count, mold and yeast counts of all samples increased gradually, and the shelf life of IRN sample with ε-polylysine hydrochloride (JL) preserved at 4 °C was significantly extended to 14 days. The pH value of sample with JL decreased gradually whereas the pH value of sample with citric acid (NM) increased slightly during storage. In IRN, molds displayed a greater spoilage potential than bacteria and yeasts. The 16S rDNA sequencing results indicated that preservatives, rather than temperature deduce to the significant differences of spoilage bacterial community among samples, and the NM considerably decreased the bacterial diversity internal transcribed spacer (ITS) region. rDNA sequencing results demonstrated that temperature was the critical factor in shaping fungal spoilage microbiota (Mantel test r = 0.16143, P < 0.05). Moreover, Spearman correlation analysis revealed that the abundance of partial microorganisms was significantly related to pH or temperature. The abundance of Achromobacter (r = −0.66276, P < 0.01), Delftia (r = −0.59983, P < 0.01), and Phyllobacterium (r = −0.55765, P < 0.01) were negatively correlated with pH. Additionally, the temperature was positively related to the relative abundance levels of Romboutsia (r = 0.517, P < 0.005), Arthrobacter (r = 0.446, P < 0.05), Bacillus (r = 0.551, P < 0.01), Bacteroides (r = 0.456, P < 0.05), and norank_f__JG30-KF-CM45 (r = 0.449, P < 0.05). These findings provided guiding information in selecting targeted preservatives and environmental condition for this innovative high moisture food.
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