Post-harvest microbiome dynamics and their impact on the safety and quality of Lupinus mutabilis sweet (Chocho)

Chocho (Lupinus mutabilis Sweet), a traditional Andean legume, undergoes diverse post-harvest handling and processing steps that can influence its microbial composition and physicochemical properties. To understand how these factors shape food safety and consumer health, we characterized the chocho microbiome across the farm-to-table chain, including field-dried grains (Group C), open-market ready-to-eat products (Group A), and supermarket grains (Group K). Bacterial and fungal communities were profiled using 16S rRNA and ITS amplicon sequencing, and moisture, pH, titratable acidity, and total alkaloids were quantified and correlated with microbial patterns. High-depth 16S rRNA sequencing (60,000–140,000 reads/sample) showed the highest bacterial diversity in Group A (Shannon = 5.23), followed by Group K (4.69) and Group C (4.08). Richness and evenness differed significantly (p < 0.05) among groups, and beta-diversity analyses (Bray–Curtis, Jaccard, UniFrac) revealed clear clustering by grain source (PERMANOVA, p ≤ 0.005). Market grains were enriched in handling-associated genera such as Pseudomonas, Flavobacterium, and Enterococcus, whereas field grains contained soil-associated taxa including Paenibacillus and Arthrobacter. Fungal profiling showed the greatest richness and phylogenetic diversity in local-producer samples, with supermarket grains displaying lower but more even communities. Xerophilic Wallemia dominated dry grains, whereas moisture-exposed market grains were enriched in spoilage yeasts (Debaryomyces, Candida, Rhodotorula). Physicochemical traits varied widely: moisture (3.7–8.7%), titratable acidity (0.09–0.59%), pH (4.9–6.2), and alkaloids (<0.5% in processed grains vs. 5–7% in field samples). PCA explained 90.6% of the variance, with alkaloids strongly correlating with acidity (r = 0.94). Several processed samples exceeded national alkaloid limits (<0.02%), indicating incomplete debittering. These findings demonstrate that environmental exposure and handling strongly influence the microbial and toxicological safety of chocho along its supply chain.