Bacterial and fungal community composition in dairy products and plant-based dairy alternatives using high throughput sequencing

The increasing consumer demand for plant-based dairy alternatives has enhanced scientific interest in understanding their microbiological characteristics, particularly in comparison to traditional fermented dairy products. This study investigated the microbiological status of commercial dairy and plant-based fermented cheese and kefir products, using classical and molecular (High Throughput Sequencing - HTS) approaches. Classical microbiological analysis revealed a noteworthy dominance of yeasts and lactic acid bacteria (LAB) in all samples tested, with yeasts prevailing in most cases and LAB co-dominating particularly in plant-based cheeses and kefirs. Notably, Enterococcus were more prominent in plant-based products, while Enterobacteriaceae and coliforms were detected exclusively in some plant-based samples, highlighting the need for a more precise fermentation control. High throughput 16S rRNA gene sequencing revealed a relatively low bacterial diversity in dairy samples, with Streptococcus and Lactococcus dominating. In contrast, plant-based products exhibited greater diversity, including beneficial families (e.g., Lactobacillaceae) or genera (e.g., Leuconostoc) and occasional spoilage-associated taxa (Raoultella, Pseudomonas). Fungal analysis showed high variability across samples, with Penicillium dominating aged cheese, Debaryomyces and Malassezia being common in both dairy and plant-based products. However, potential environmental and/or potential pathogenic fungi (e.g., Cladosporium, Neorysiphe) were detected in some plant-based products, reflecting raw material origin and/or insufficient processing controls. Overall, dairy products exhibited consistent, fermentation-driven microbiota, while plant-based samples showed higher microbial complexity, including both functional and potentially undesirable microorganisms. The findings emphasize the unique microbial characteristics of each product type, underscoring the need for targeted microbial management and the selection of appropriate starter culture in plant-based fermentations to ensure both safety and functional benefits, supporting innovation and quality control in the growing dairy alternative sector. This research contributes valuable knowledge for producers, regulators, and other stakeholders, as well as health-conscious consumers navigating the evolving plant-based dairy landscape, providing in parallel a noteworthy technological and scientific background, so that help the industry to provide innovative, safe and high-quality plant-based dairy products to the international commerce.