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Key research themes
1. How do molecular and culture-independent methods enhance understanding of cheese microbiota diversity and activity?
This research theme focuses on the development and application of molecular techniques, such as 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and RNA-based analyses, to characterize the composition, metabolic activity, and dynamics of cheese-associated microbial communities. It addresses the limitations of traditional culture-dependent methods and explores how integrative molecular approaches enable detailed profiling of both cultivable and uncultivable bacteria, yeasts, and molds, thereby linking microbial populations to cheese ripening processes, safety, and organoleptic properties. Understanding these microbial interactions and activity patterns is critical for controlling cheese quality and flavor development, as well as for identifying functional microbiota in artisanal and industrial cheese production.
Key finding: The paper reviews how combining culture-dependent and independent methods, especially DNA- and RNA-based analyses coupled with polyphasic approaches, improves identification of metabolically active microbial populations in... Read more
Key finding: Applied culture-dependent and independent techniques, including 16S rRNA gene amplicon sequencing combined with propidium monoazide (PMA) treatment, revealed viable microbial communities in raw, pre- and post-pasteurization... Read more
Key finding: This editorial synthesizes multidisciplinary advances illustrating how combinations of microbiological, compositional, and biochemical analyses—including molecular methods—are employed to study cheese production and ripening.... Read more
Key finding: The review stresses that combining culture-dependent and high-throughput DNA/RNA sequencing methods, along with multi-omics technologies, is essential to capture the dynamic establishment and interactions of starter and... Read more
Key finding: By employing both DGGE and pyrosequencing of 16S/26S rRNA genes, this study tracked microbial succession on cheese surfaces and interiors during production and ripening. It demonstrated that deep sequencing surpasses DGGE in... Read more
2. What roles do specific microbial taxa and contamination sources play in cheese spoilage and defects?
This research area investigates identification and confirmation of bacterial species and consortia responsible for spoilage phenomena—such as slit defects in Cheddar cheese—as well as the microbial ecology driving cheese rind microbiomes. Studies use a combination of microbiological enumeration, molecular sequencing, and culturing to map microbial transmission pathways from milk and environmental reservoirs to cheese, assessing viable populations and their contribution to defects. Understanding these causes enables better control of microbial contamination, reduces economic losses, and guides hygienic and manufacturing interventions.
Key finding: The study identified specific non-starter lactic acid bacteria and Clostridium species from viable cells in raw and pasteurized milk that cause slit defects in Cheddar cheese. It showed that slit formation is unpredictable... Read more
Key finding: High-throughput pyrosequencing revealed a complex bacterial community dominated by Lactococcus and core taxa including Streptococcus, Lactobacillus, and Enterococcus throughout Pico cheese maturation. Statistical differences... Read more
Key finding: By isolating and characterizing virulent bacteriophages infecting core rind bacterial species, including Brevibacterium and Glutamicibacter, and detecting identical phages on cheese factory surfaces, this study linked phage... Read more
Key finding: The characterization of Picante cheese microbiota over a 180-day ripening period identified dominant species within Enterobacteriaceae, staphylococci, enterococci, lactobacilli, and yeasts, highlighting diverse microbial... Read more
3. How do microbial communities and environmental microbiota shape artisanal cheese typicity and ripening outcomes?
This theme explores how indigenous microbial ecosystems from milk, backslopping cultures, and cheese-making or ripening environments impact the sensory characteristics, aroma profiles, and typicity of artisanal cheeses. Research addresses the origin, succession, and functional roles of lactic acid bacteria, yeasts, molds, and their interactions, including production of volatile organic compounds (VOCs) influencing flavor development. These studies also consider how facility-specific 'house' microbiota contribute to brand specificity and natural inoculation during ripening, connecting microbiota structure with biochemical and organoleptic properties key for preserving cheese uniqueness.
Key finding: Combining 16S rRNA gene sequencing and environmental sampling, the study showed that facility-specific microbiota, including Staphylococcus equorum and Brevibacterium, dominate cheese rinds and adjacent processing surfaces.... Read more
Key finding: Using combined culture-dependent and independent (MALDI-TOF and metabarcoding) approaches alongside volatilome analyses, the study correlated microbial succession during Pélardon cheese-making with biochemical changes,... Read more
Key finding: The study demonstrated that fungal-derived volatile organic compounds (VOCs), particularly acetate-containing volatiles, promote the growth of Vibrio species and alter chicken rind microbial community assembly. Transcriptomic... Read more
Key finding: Through combined culture-based and non-culture DNA approaches, the research tracked microbial population growth and diversity during May bryndza cheese manufacturing and ripening, highlighting dominant lactic acid bacteria... Read more
Key finding: The metataxonomic analysis coupled with viable counting and enzymatic profiling revealed dominant species including Lactococcus lactis and diverse Enterococcus spp. in Queijo Serra da Estrela cheeses. Detailed volatile... Read more