A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter

Abstract

IntroductionIn Kimoto-style fermentation, a fermentation starter is produced before the primary brewing process to stabilize fermentation. Nitrate-reducing bacteria, mainly derived from brewing water, produce nitrite, and lactic acid bacteria such as Leuconostoc can proliferate because of their tolerance toward low temperature and their low nutritional requirements. Later, Lactobacillus becomes the dominant genus, leading to weakly acidic conditions that contribute to control yeasts and undesired bacterial contaminants. However, the sources of these microorganisms that play a pivotal role in Sake brewing have not yet been revealed. Thus, comprehensive elucidation of the microbiome is necessary.MethodsIn this study, we performed 16S rRNA amplicon sequencing analysis after sampling from floor, equipment surfaces, and raw materials for making fermentation starters, including koji, and water in Tsuchida Sake brewery, Gunma, Japan.ResultsAmplicon sequence variants (ASVs) between the external environments and the fermentation starter were compared, and it was verified that the microorganisms in the external environments, such as built environments, equipment surfaces, and raw materials in the sake brewery, were introduced into the fermentation starter. Furthermore, various adventitious microbes present in the fermentation starter of early days and from the external environments were detected in a nonnegligible proportion in the starter, which may impact the taste and flavor.DiscussionThese findings illuminate the uncharacterized microbial dark matter of sake brewing, the sources of microbes in Kimoto-style fermentation.

The similarities in microbial and chemical patterns of fermentation in two open environments were promoted by using 150-year-old Nukadoko as starters

“…Our results showed that Loigolactobacillus , an anaerobic, homo-fermentative bacteria, became dominant in both environments. Similarly, in another study, Loigolactobacillus was identified as the dominant genus in nukadoko samples (Niwa, Chen et al ., 2023). The process through which adventitious bacteria are outcompeted by LAB at the later stages of fermentation is dependent on the types of LAB that dominate the microbiome (Ono et al ., 2014).…”

“…Indeed, within the architectural environment in which the samples are placed, various microbes, known as the Microbiome of the Built Environment (MoBE), exist, which can influence the production of fermented foods (Gilbert and Stephens, 2018;Ito, 2023) . MoBE has been found to contaminate the fermentation starter in a sake brewery (Ito, Niwa, Kobayashi, et al , 2023) . Similarly to the effects of Lactobacillus dominance of the microbiome in other experiments involving nukadoko , the presence of Loigolactobacillus in our experiment may also provide stability to the fermentation process and prevent adventitious microbes from contaminating the nukadoko environment.…”

Comparative analysis based on shared amplicon sequence variants reveals that cohabitation influences gut microbiota sharing between humans and dogs

“…However, these analyses did not determine whether the same bacteria were transferred or shared. To precisely evaluate the sharing of the gut microbiota between humans and dogs, we conducted a shared ASV analysis, which is an approach for inferring the sharing ratio of the microbiome at the ASV level between samples and has been used previously (31,40,41). While the sharing of ASVs was not detectable after two weeks of cohabitation, it was observed in the first and third months.…”

Bioinformatic evaluation of the potential oral-gut translocation of periodontal pathogens in patients with colorectal polyps

“…Shared ASVs analysis was performed based on a previous study 26,27 . We defined shared ASVs as ASVs shared by >1.0% of both samples in this study.…”