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Dadih is an Indonesian traditional spontaneously fermented buffalo milk, produced in West-Sumatra, which is nutritious and has health benefits. The mechanism of action behind the health benefits is largely unknown, but several probiotic strains have been isolated from dadih, which may contribute to its health properties. To identify the composition of its microbiota, two artisanal dadih samples (n = 8) were collected from four producers. The raw buffalo milk used for fermentation was either pasteurized (n = 4) or not (n = 4), and back-slopping was used as a starter-culture (n = 5) or not (n = 3). DNA was extracted from each sample in duplicate and the microbiota composition was determined by 16S-rRNA-gene amplicon-sequencing of the V3-V4 region. PCoA analysis showed clear separation of the samples by producer, but no separation due to pasteurization or use of back-slopping. Lactococcus (52-83%) predominated in all samples, followed by Klebsiella (5-26%), and Lactobacillaceae, Bifidobacterium (particularly high (c. 18%) in the non-pasteurized, back-slopped product from Palupuh), Streptococcus and Leuconostoc. Back-slopping practice correlated significantly with higher abundance of Lactobacillaceae, Pediococcus, species of the order Burkholderiales, and Serratia, but with lower abundance of several other Enterobacteriaceae (including Klebsiella), Streptococcaceae, Staphylococcus and Brachybacterium. Pasteurization was not significantly correlated with the presence of certain members of the final microbiota. Taken together, fermentation results differ significantly from producer to producer and back-slopping practice would be advisable. SIGNIFICANCE AND IMPACT OF THE STUDY: Using state-of-the-art methods we determined the microbiota composition of dadih, an artisanal, traditional fermented buffalo milk of West Sumatra with health benefits. We show that the artisanal practice leaves room for standardization and optimization with respect to the presence of potential pathogenic species in the final product. The Dadih Initiative in Indonesia aims to expand production of this health promoting product, and the findings help to determine important steps for potential food safety issues and good-manufacturing-practices to obtain a safe, nutritious and healthy traditional yoghurt-like functional food.
Pubmed ID: 30565283
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Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized.
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