Agricultural by-products such as apricot kernel shells (AKS) and walnut shells (WS) constitute a substantial portion of global food waste generated by processing industries. The shell composition has potential for sustainable industrial applications that align with circular economy goals. Microbial communities present on AKS and WS surfaces, or those introduced during postharvest handling and storage, may pose significant contamination. Monitoring microbial quality should be considered before repurposing as raw ingredients for cosmetic and food-related applications. Kyrgyzstan is a key Central Asian country for the natural agroforestry of walnuts and apricot agroforestry with integrated co-agriculture practices. We investigated the microbial communities associated with AKS and WS collected from Kyrgyzstan over three harvest years (2022–2024), using comparative samples from German supermarkets and an online platform. To assess microbial load, taxonomic diversity, and functional potential of the detected microorganisms on the shell surfaces, culture-dependent total viable count analysis and culture-independent shotgun metagenomic sequencing were employed. Harvest-dependent variations in microbial load were observed, with Proteobacteria dominant on WS, including Pantoea agglomerans and Xanthomonas arboricola. In contrast, AKS samples were dominated by the phylum Firmicutes, particularly Weissella confusa and Weissella cibaria. Three-month storage of shells at 20°C with 50% relative humidity led to noticeable changes in fungal diversity.
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