Microbiota community structure in traditional fermented milk dadiah in Indonesia: Insights from high-throughput 16S rRNA gene sequencing
Keywords:
Dadiah, fermented buffalo milk, deep sequencing, 16S ribosomal RNA, microbiotaAbstract
Dadiah is an Indonesian traditional fermented milk and is neither pasteurized nor boiled, but no food poisoning has been reported to date. Microbiota inhabiting dadiah has never been fully explored. In this study, we performed deep sequencing of 16S ribosomal RNA genes extracted from 11 dadiah samples and analyzed the dadiah microbiota at the genus level. We found that Lactococcus, Lactobacillus, and Leuconostoc were predominant among the dadiah microbiota. Unexpectedly, Klebsiella and Chryseobacterium, potential pathogens, were also found in some of the dadiah samples. There was little difference in the microbiota among samples taken from the same bamboo tube. In contrast, there were differences between the dadiah microbiota from different bamboo tubes, even those collected from the same sampling area. Furthermore, the composition of the dadiah microbiota showed large differences between sampling areas. We believe that our findings will lead to further improvement in the preparation of dadiah.
References
Quigley L, O’Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, et al. The complex microbiota of raw milk. FEMS Microbiol Rev. 2013;37(5):664–98.
Surono IS. Traditional Indonesian dairy foods. Asia Pac J Clin Nutr. 2015;24:S26–30.
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform. Appl Environ Microbiol. 2013;79(17):5112–20.
Morita H, Kuwahara T, Ohshima K, Sasamoto H, Itoh K, Hattori M, et al. An improved DNA isolation method for metagenomic analysis of the microbial flora of the human intestine. Microbes Environ. 2007;22(3):214–22.
Said HS, Suda WA, Nakagome SH, Chinen HI, Oshima KE, Kim SA, et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res. 2014;21(1):15–25.
Klindworth A, Pruesse E, Schweer T, Peplis J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–7.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):590–6.
Field A. Discovering statistic using SPSS. 3rd ed. London: Sage Publication Ltd. 2009. p. 671.
Surono IS, Nurani D. Exploration of indigenous dadih lactic bacteria for probiotic and starter cultures. Domestic research collaborative grant-URGE-IBRD World Bank Project 2000-2001 Republic of Indonesia: Directorate General of Higher Education, Ministry of Education and Culture. 2001. p. 24.
Martin NH, Trmcic A, Hsieh TH, Boor KJ, Wiedmann M. The evolving role of coliforms as indicators of unhygienic processing conditions in dairy foods. Front Microbiol. 2016;7:1549.
Vishnu TS, Soniyamby AR, William A, Abhinand RL, Praveesh B V. A minireview of an opportunistic pathogen- Chryseobacterium sp. World J Pharm Pharm Sci. 2014;3(4):599–605.
Staley C. Dunny GM. Sadowsky MJ. Environmental and animal-associated enterococci. Adv Appl Microbiol. 2014;87:147–86.
