Title : Sip smart: What shotgun metagenomics tells us about fermented oat concentrates
Abstract:
Understanding the microbial dynamics and functional potential of fermentation microbiota is crucial for optimizing product quality, ensuring food safety, and advancing the development of health-promoting functional beverages. Traditional microbiological methods and 16S rRNA sequencing have been widely used to describe microbial communities in fermented foods; however, these approaches are limited in taxonomic resolution and often fail to capture the functional complexity of microbial ecosystems. Shotgun metagenomic sequencing has emerged as a powerful method that provides direct access to the total DNA of microbial consortia, enabling high-resolution taxonomic identification as well as metabolic and functional pathway prediction. This approach is particularly valuable for studying non-dairy fermented products, such as oat-based beverages, which are characterized by diverse and substrate-specific microbiota.
In this study, shotgun metagenomic sequencing was applied to characterize the microbial structure and functional gene profiles of fermented oat-based products (FPs). Quality control and host DNA filtering resulted in over 97% high-quality effective reads, exceeding the commonly reported range (70–90%) in similar studies. The number of assembled scaffolds varied from 78,746 to 867,039 per sample, with maximum contig lengths up to 933,637 bp, indicating robust data suitable for detailed analysis. Taxonomic annotation was performed using the MicroNR database, alpha diversity was assessed by Shannon and Simpson indices, and functional profiling included analyses based on the CAZy (Carbohydrate-Active Enzymes) and PHI (Pathogen–Host Interaction) databases.
Metagenomic analysis revealed that bacterial taxa dominated all oat-based products, primarily Lactobacillus, Limosilactobacillus, Clostridium, and Klebsiella species. The blackcurrant-based sample (FP6) displayed the highest abundance of Limosilactobacillus fermentum (65.7%) and the yeast Pichia californica, alongside notable quantities of bacteriophages (Caudoviricetes sp.). Alpha diversity indices indicated a rich and balanced microbiota in the oat–blackcurrant fermented probiotic drink concentrate (FP2) (Shannon index 3.99) and lower diversity in FP6 (1.62). CAZy functional analysis identified six major enzyme classes, with glycoside hydrolases (GH) and glycosyltransferases (GT) being predominant. These enzymes play vital roles in carbohydrate degradation, nutrient bioavailability, and texture development during fermentation. PHI gene analysis indicated that FP6 and the oat-flavored bacterial concentrate (FP7) samples harbored the highest abundance of genes involved in pathogen–host interactions, suggesting potential antimicrobial and probiotic properties.
Conclusions: This study provides new insights into the microbiome structure and functional potential of fermented oat-based beverages using shotgun metagenomics. The results demonstrate that microbial composition and enzyme activity profiles vary significantly among products, reflecting the influence of fermentation substrates. The dominance of Lactobacillus spp. and the diversity of carbohydrate-active enzymes highlight the key role of microbial metabolism in determining product functionality. These findings contribute to a deeper scientific understanding of plant-based fermentations and establish a foundation for developing next-generation functional and probiotic beverages.
Keywords: shotgun metagenomics; fermented oat beverage; microbiota; probiotic potential; CAZy enzymes; PHI genes; functional food
