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. 2025 Aug 18;12(3):717-727.
doi: 10.5455/javar.2025.l935. eCollection 2025 Sep.

Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia

Evy Rossi  1 , Usman Pato  1 , Dewi Fortuna Ayu  1 , Sri Melia  2 , Ade Sukma  2 , Rahmayuni Rahmayuni  1 , Annisa Nazifa Salman  1
Affiliations

Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia

Evy Rossi et al. J Adv Vet Anim Res. .

Abstract

Objective: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.

Materials and methods: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.

Results: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.

Conclusion: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.

Keywords: Dadih; buffalo milk; fermentation; metagenomic; next-generation sequencing.

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Conflict of interest statement

The authors affirm that there are no conflicts of interest in this paper.

Figures

Figure 1.
Figure 1.. The location of dadih sampling in Kampar Regency, Riau, Indonesia.
Figure 2.
Figure 2.. The dominant phylum in dadih from LM = Limau Manis, RB = Rumbio, and MJ = Muaro Jalai. The color degradation of each column shows the abundance of phyla in each Dadih.
Figure 3.
Figure 3.. Distribution of bacterial species present in dadih produced from LM = Limau Manis, RB = Rumbio, and MJ = Muaro Jalai.
Figure 4.
Figure 4.. Heatmap species of dadih produced from LM = Limau Manis, RB = Rumbio, and MJ = Muaro Jalai.
Figure 5.
Figure 5.. The relative proportion of phyla to species of dadih bacteria from Limau Manis village, Kampar district, Riau, Indonesia.
Figure 6.
Figure 6.. The relative proportion of phyla to species of dadih bacteria from Rumbio village, Kampar district, Riau, Indonesia.
Figure 7.
Figure 7.. The relative proportion of phyla to species of dadih bacteria from Muaro Jalai village, Kampar district, Riau, Indonesia.
Figure 8.
Figure 8.. Venn diagram of the distribution of bacterial OTUs in dadih produced from LM = Limau Manis, RB = Rumbio, and MJ = Muaro Jalai.
Figure 9.
Figure 9.. Evenness (Shannon) and richness (Simpson) of dadih produced from LM = Limau Manis, RB = Rumbio, and MJ = Muaro Jalai.
Figure 10.
Figure 10.. The PCoA of the weighted UniFrac (beta diversity) in the lactic acid bacteria of dadih.
See this image and copyright information in PMC

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