The microbiota of wild fermented cider from U.S. west coast apples

Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.