Nanopore sequencing enables detailed metagenomics of closely related bacterial strains used in the dairy industry
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Diacetyl, acetoin, acetate, acetaldehyde and ethanol are central compounds for the quality and distinct flavor profile of many dairy products. These compounds are produced during complex fermentation processes. Understanding such processes are far from trivial, as important technological properties differ at the bacterial strain level interactions playing a strong role for final quality. Many dairy products (e.g., buttermilk and many cheese types) are produced using undefined starter cultures containing several different species further divided into dozens of different strains. Recent developments in long read DNA sequencing offered by Oxford Nanopore Technologies give new opportunities to study complex microbial cultures with precision never seen before. Detailed genomics combined with high-resolution data on aroma formation during fermentations opens new possibilities for developing machine learning-based tools.
We have recovered full, complete genomes (including plasmids) of 60 bacterial strains from a mesophilic starter culture used for fermentation of dairy products. Detailed metagenomics disclosed pivotal, unique, strain specific features of closely related bacteria. This includes unique phage resistance mechanisms, mobile elements and gene clusters playing role in flavour formations of dairy products.