Metagenomic analysis of 130 years old Danish starter culture material including sequence analysis of the genome of a Lactococcus cremoris starter

Abstract

Two unopened Danish dairy starter culture bottles from the 1890s were analyzed to investigate their microbiome and genetic characteristics, offering insights into historical dairy production. Using culture-independent methods, DNA was extracted and sequenced via Nanopore-based Barcode-Amplified Random Sequencing. Metataxonomic profiling revealed contamination with Cutibacterium acnes, while the 1893 sample showed significant Lactococcus cremoris DNA (76.7 % genome coverage), compared to minimal coverage (<1 %) in the 1899 sample. Bioinformatic analysis identified functional genes in L. cremoris associated with dairy adaptation, including casein degradation, lactose metabolism, and acetoin/diacetyl production, which contribute to buttery flavors. These findings are of interest, considering mild flavor profile preferred in Danish butter for the English market during the 19th century. Additionally, a conserved lactococcin gene (lcn) was detected in both the 1893 sample and a modern isolate of L. Cremoris, suggesting its persistence over time. This study sheds light on the microbiome and functional properties of historical starter cultures.