Metagenomic Characterization of the Culturable Bacterial Community Structure of Tapuy, a Philippine Indigenous Rice Wine, Reveals Significant Presence of Potential Probiotic Bacteria

  • Thea Coleen F. Sanico UP Manila College of Medicine
  • Paul Mark B. Medina
Keywords: bacterial community structure, food microbiology, fermented foods and beverages, wine, tapuy, targeted metagenomics


Background. Tapuy is an indigenous fermented rice wine produced in the Northern areas of the Philippines. Fermented foods and drinks have gained interest due to their associated health benefits, attributable to probiotic bacteria in the food items. However, pathogenic bacteria may also be present in fermented food and pose health risks, signifying a need for standardization. Currently, there is limited knowledge on the bacterial content of tapuy.

Objectives. This study aimed to characterize the bacterial diversity and community structure of culturable bacteria in traditionally fermented tapuy samples, to perform standardization of tapuy fermentation, and to compare the bacterial diversity and community structure of culturable bacteria in laboratory fermented tapuy with that of the traditional samples.

Methods. Tapuy samples were obtained from four municipalities in Benguet, Philippines. Laboratory fermentation of tapuy was performed simultaneously with the fermentation in the sampling site using a standardized protocol. Samples were plated on de Man, Rogosa, and Sharpe (MRS) agar and NA, and the colonies were harvested for DNA extraction. DNA samples were sent for 16S rDNA metagenomic sequencing.

Results. Metagenomic analysis revealed the presence of many bacterial species that were previously unreported in tapuy. Traditional tapuy samples were composed primarily of members of the genera Bacillus and Lactobacillus in varying proportions. Potential probiotic bacteria were abundant in Kapangan (97.42%) and Sablan (99.89%) field samples. B. wiedmannii was present in all samples and was identified as a harmful species. Laboratory fermentation increased the abundance of potential probiotic bacteria in Itogon and La Trinidad samples (differences of 75.36% and 78.36%, respectively). It decreased the quantity of B. wiedmannii in La Trinidad (a difference of 97.1%). Laboratory fermented samples generally exhibited higher bacterial diversity and species richness compared to field samples. Conclusions. Traditionally fermented tapuy samples contained a significant proportion of potential probiotic bacteria belonging to the genera Bacillus and Lactobacillus. Laboratory fermented samples were found to have higher bacterial diversity and richness compared to field samples. The significant presence of potential probiotic bacteria suggests that tapuy is a good candidate for development into functional food and a good source of likely probiotic species that could be explored for health applications. The presence of harmful bacteria suggests the need for possible standardization of fermentation practices.