Metagenomic analysis of bacterial community composition in Dhanaan: Ethiopian traditional fermented camel milk

Abstract

This study was conducted to evaluate the safety and bacterial profile of Dhanaan (Ethiopian traditional fermented camel milk). The composition of the microbial community in Dhanaan samples was analysed by a metagenomic approach of 16S rRNA gene amplicon sequencing. Metagenomic profiling identified 87 different bacterial microorganisms (OTUs) in six samples analysed. Although the Dhanaan samples contained various lactic acid bacteria (LAB), they also all contained undesirable microorganisms in large proportions. The following LAB genera were identified: Streptococcus, Lactococcus and Weissella. One Streptococcus species represented by OTU-1 (operational taxonomic unit) was found in all Dhanaan samples and the dominating species in four out of six samples. This common isolate was found to be closely related to S. lutetiensis and S. infantarius. Undesirable microorganisms from genera such as Escherichia, Klebsiella, Enterobacter, Acinetobacter and Clostridium were, however, also frequent, or even dominant in Dhanaan samples. Thus, this calls for a change in the Dahnaan manufacturing practice to an improved and safer production system. Starter cultures suitable for Dhanaan production might be developed from the Streptococcus, Weissella and Lactococcus microorganisms identified in this study. However, further safety evaluation and technological characterization need to be conducted on strains defined by OTU-1, OTU-2, OTU-3, OTU-8 and OTU-35 before they can be used as food grade starter cultures.