Tempe microbiome across Indonesia

Fermenting food for dietary purposes has a long history in human civilization and yields a wide range of products. Tempe, a soybean product from Indonesia, is created through fermentation by Rhizopus spp. and associated bacteria. Here, we aim to get an overview of the variability of the tempe microbiota across Indonesia and to disentangle influencing factors. Altogether, we found surprisingly high variability in bacterial abundance (103 – 109 copies g-1), richness (nASV=40 – 175 ASVs), and diversity (H' = 0.9 – 3.5) in Indonesian tempe. The primary factor affecting this variation was the region, where the tempe was produced. Interestingly, tempe samples obtained from geographically close areas tended to share similar bacterial profiles, suggesting a distinctive regional characteristic or "terroir" of tempe. Additionally, we observed that the choice of packing material (banana leaves or plastic) also had a significant impact. Tempe wrapped in leaf had a higher abundance of enterobacteria in comparison to tempe wrapped in plastic but also tended to have a higher total bacterial and lactobacilli. In contrast, the relative abundance of Staphylococcus was higher in tempe wrapped in plastic (4.3%) in comparison to tempe wrapped in leaves (0.9%). Despite all variability, the tempe microbiota is characterized by an abundant and dominant core comprising taxa of Lactobacillales and Enterobacteriales. These findings confirm the expected diversity of traditional tempe, and highlight the strong regional influence observed across Indonesia. Furthermore, our results support the traditional and environmentally friendly practice of packaging tempe in banana leaves, as it promotes the growth of beneficial microorganisms and suppresses the presence of harmful pathogens in the product.