The terroir of Tempeh: Strong region-specific signatures in the bacterial community structures across Indonesia

Abstract

Tempeh, 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 tempeh microbiota across Indonesia and disentangle influencing factors. We found high variability in bacterial abundance (10³ - 10⁹ copies g^-1), richness (n_ASV = 40 - 175 ASVs), and diversity (H' = 0.9 - 3.5) in tempeh. The primary factor affecting this variation was the region, where the tempeh was produced. Interestingly, tempeh samples obtained from geographically close areas tended to share similar bacterial profiles, suggesting a "terroir" of tempeh. Additionally, tempeh wrapped in banana leaves had a higher abundance of enterobacteria in comparison to tempeh wrapped in plastic but also tended to have a higher total bacterial and lactobacilli abundance. Despite all variability, the tempeh core microbiome consists Lactobacillales and Enterobacteriales. This study demonstrates a high variability of bacterial diversity in traditional tempeh from local producers highlighting a strong regional influence across Indonesia.

Keywords: Amplicon sequencing; Fermented food; Lactobacilli; Microbiome; Tempeh; Terroir.

Graphical abstract

Fig. 1

Summary of sampling location and the conducted microbial community analyses.

Fig. 2

Comparison of bacterial abundance and diversity between tempeh collected from different geographical origins and with different packaging. Total bacterial (A), lactobacilli (B), and enterobacterial (C) abundance were measured using a qPCR-based method. Number of bacterial ASVs (D) and Shannon index (E) were calculated from the high-throughput amplicon sequencing.

Fig. 3

Bacterial community compositions of tempeh collected from different geographical origins and with different packaging. The nonmetric multidimensional scaling (NMDS) plots show the clustering of bacterial communities from tempeh wrapped in leaves (A) and plastic (B). Hierarchical clustering of bacterial community compositions of tempeh collected from different cities indicates clusters based on the provinces.

Fig. 4

Comparative assessment of bacterial community composition and tempeh core microbiome. Bar plot represents bacterial composition at genus level (A). A phylogenetic tree was constructed with partial 16S rRNA gene of the core microbiome (B). City of origin – BAN: Bandung, JAK: Jakarta, SLE: Sleman, KEB: Kebumen, DEN: Denpasar, and SING: Singaraja.

Fig. 5

A correlation network analysis (Pearson's correlation) of bacterial communities in tempeh wrapped in leaves (A) and plastic (B). Node sizes represent the relative abundance of bacterial genera and the thickness of lines connecting nodes represents the value of Pearson's correlation coefficients.