Characteristics of bacterial and yeast microbiomes in spontaneous and mixed-fermentation beer and cider

• Published in: Food microbiology 2021-04, Vol.94, p.103658-103658, Article 103658
• Main Authors: Tyakht, Alexander, Kopeliovich, Anna, Klimenko, Natalia, Efimova, Daria, Dovidchenko, Nikita, Odintsova, Vera, Kleimenov, Mikhail, Toshchakov, Stepan, Popova, Alexandra, Khomyakova, Maria, Merkel, Alexander
• Format: Article
• Language: English
• Subjects: Alcoholic Beverages - analysis; Alcoholic Beverages - microbiology; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Beer; Beer - analysis; Beer - microbiology; Cider; Fermentation; Food Microbiology; High-throughput sequencing; Malus - microbiology; Microbiome; Microbiota; Non-conventional yeasts; Spontaneous fermentation; Yeasts - classification; Yeasts - genetics; Yeasts - isolation & purification; Yeasts - metabolism
• ISSN: 0740-0020; 1095-9998
• DOI: 10.1016/j.fm.2020.103658

The production of experimental beer and cider products has increased, worldwide. The complex microbiomes found in these beverages affect their organoleptic qualities and chemical compositions and can have diverse impacts on human health. The total diversity of a microbiome can be elucidated through the use of high-throughput sequencing and comprehensive data analysis tools. We analysed the bacterial and yeast microbiomes found in mixed and spontaneously fermented beers (n = 14) and unpasteurised apple ciders (n = 6), using high-throughput 16S rRNA and internal transcribed spacer (ITS) sequencing. The ratio of bacteria to yeast was measured using quantitative polymerase chain reaction (qPCR), and short-chain organic acids were analysed using high-performance liquid chromatography (HPLC). An upgraded version of the Knomics-Biota system was used to analyse the data. The microbiomes included both starter microorganisms and those that originate from the production environment and the raw materials. In addition to the common Saccharomyces and Brettanomyces, the yeast diversity included many non-conventional species. The bacterial community in beer was dominated by Lactobacillus species, whereas these communities were more diverse in cider. Lactobacillus acetotolerans was prevalent in wild ales, whereas Candida ethanolica was prevalent in cask-matured beverages. We observed complex patterns of subspecies-level yeast diversity across beer styles, breweries, and countries. Our study represents an exploratory analysis of non-conventional beer and cider microbiomes and metabolomes, which contributes information necessary to develop improved quality control processes and may drive innovative product development in experimental and artisanal brewing. •The microbiomes in spontaneous beer and cider are diverse.•We observed complex patterns in the occurrence of yeast subspecies across beer styles and breweries.•The bacterial communities found in beer are dominated by various Lactobacillus species, whereas cider demonstrates higher species diversity.•Lactobacillus acetotolerans was prevalent in wild ales, whereas Candida ethanolica was prevalent in cask-matured beverages.•16 S rRNA/ITS sequencing, combined with metabolomics and interactive data analysis, represents a promising tool for improving quality control and innovations in brewing.