NGS profiling of bacterial, archaeal and fungal communities in winery liquid effluents used for Chlorella cultivation (REDWine project)

The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard–winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples collected at a winery in the Setúbal Peninsula, Portugal. Metagenomic analysis targeting the 16S rRNA gene was used to characterize microbial diversity and identify taxa with potential relevance for biotechnology and environmental applications. The effluents exhibited a diverse microbiome, including Prevotella paludivivens, species from the Lactobacillus genus, and members of the Clostridiaceae family, the latter representing about 5% of the total community. Functional profiling of lactic acid bacteria revealed the predominance of Oenococcus and Lactobacillus genera, highlighting adaptive traits that may be beneficial under stress conditions. These results suggest that winery effluents, often considered waste, harbor microbial communities with functional potential that extends beyond fermentation, contributing to a broader grape–wine microbial system. The findings emphasize the value of studying winemaking by-products as reservoirs of microbial diversity and as resources for developing innovative and sustainable applications in biotechnology and environmental management within the wine industry.