Microbiota and Cheese Quality

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 218

Special Issue Editors


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Guest Editor
Food Technology Area, Faculty of Science, University of Vigo, Ourense, Spain
Interests: dairy technology; dairy microbiology; cheese making; cheese ripening; cheese flavor; lactic acid bacteria; adjunct cultures; traditional cheeses
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Dear Colleagues,

Cheese is a complex microbial ecosystem comprising microorganisms that are deliberately added to or enter the milk, curd, or cheese surface as contaminants. The cheese microbiota varies depending on factors such as geographic and climatic conditions, season, manufacturing processes, and the use of raw or pasteurized milk in cheese making. In order to control cheese ripening and quality, the first and most focused approach would lie in the selection of autochthonous microbial cultures, returning them to cheesemakers for the production of different cheese varieties. This choice would be of particular interest in production where the use of raw milk is restricted or where raw milk has undergone an improvement in its microbiological quality and a modification of its “traditional” microbiota. The use of selected adjunct microbial cultures may enhance the typicality and achieve greater differentiation of Protected Designation of Origin cheeses, bringing their appearance, texture, and flavour closer to those of traditional products.

In many cheese varieties, different species and strains of yeasts, surface bacteria, lactic acid bacteria (LAB), and/or moulds can exhibit symbiotic effects that promote the development of organoleptic characteristics. Therefore, it seems essential to investigate the interactions in these complex ecosystems by using culture-independent methods. A range of molecular PCR-based techniques will undoubtedly aid in the appropriate selection of microbial cultures as well as in the monitoring of microbiota dynamics and their impact on cheese ripening and quality. Multi-omics approaches facilitate the more-accurate identification of the cheese “microbiome” and its contribution to the development of specific sensory properties. High-throughput sequencing technologies in conjunction with targeted metabolomics could be used to screen indigenous microorganisms that could have potential uses as starter or adjunct cultures in cheese production via “precision fermentation” processes (formerly referred to as “tailor-made” cultures). The association between volatile compounds (“volatilome”) and metagenomic clusters of the species represents a novel system for studying flavour development in cheese.

Finally, we must not forget the aspects concerning the microorganisms present in cheese with regard to their beneficial effects on consumer health. Cheese is generally considered a suitable carrier for probiotics into the human intestine. Numerous LAB strains with probiotic characteristics are used as starter cultures in cheese making. The use of probiotic microorganisms (LAB and bifidobacteria) to produce functional cheeses has also been reported in numerous studies.

Prof. Dr. Juan Antonio Centeno
Prof. Dr. Javier Carballo
Guest Editors

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Keywords

  • cheese microbiology
  • cheese ripening
  • lactic acid bacteria
  • adjunct cultures
  • secondary microbiota
  • cheese quality

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Published Papers (1 paper)

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20 pages, 1381 KiB  
Article
Microbial and Biochemical Analyses of High-Quality, Long-Ripened, Blue-Veined Cabrales Cheese
by Javier Rodríguez, Paula Rosa Suárez, Souvik Das, Lucía Vázquez, Sonam Lama, Ana Belén Flórez, Jyoti Prakash Tamang and Baltasar Mayo
Foods 2025, 14(13), 2366; https://doi.org/10.3390/foods14132366 - 3 Jul 2025
Viewed by 136
Abstract
Sixteen long-ripened, high-quality Cabrales cheeses from independent producers underwent a comprehensive biochemical and microbiological characterisation. Significant variations in total microbial counts and specific microbial groups were observed among the cheeses. A metataxonomic analysis identified 249 prokaryotic amplicon sequence variants (ASVs) and 99 eukaryotic [...] Read more.
Sixteen long-ripened, high-quality Cabrales cheeses from independent producers underwent a comprehensive biochemical and microbiological characterisation. Significant variations in total microbial counts and specific microbial groups were observed among the cheeses. A metataxonomic analysis identified 249 prokaryotic amplicon sequence variants (ASVs) and 99 eukaryotic ASVs, respectively, which were classified into 52 prokaryotic and 43 eukaryotic species. The predominant species included bacteria of the genera Tetragenococcus, Lactococcus (of which Lactococcus lactis was used as a starter), and Staphylococcus, followed by Brevibacterium and Corynebacterium species. The starter mould Penicillium roqueforti was highly abundant in all cheeses; Debaryomyces hansenii, Geotrichum candidum, and Kluyveromyces spp. constituted the subdominant fungal populations. Glutamic acid (≈20 mg g−1) was the most abundant free amino acid in all samples, followed by lysine, leucine, and valine (≈10–13 mg g−1). Moderate-to-high amounts of the biogenic amines tyramine and ornithine were detected. A large variation between cheeses of the main organic acids (lactic, acetic, or butyric) was detected. Differences between samples were also observed for the majority volatile compounds, which included organic acids, alcohols, esters, and ketones. Positive and negative correlations between bacterial and fungal species were detected, as well as between microbial populations and key biochemical markers. Among the latter, Tetragenococcus halophilus correlated positively with ethyl caprylate and hexanoic acid, and Loigolactobacillus rennini correlated positively with γ-aminobutyric acid. Conversely, Staphylococcus equorum showed a strong negative correlation with ethyl caprylate and capric acid. These microbial and biochemical insights enabled us to propose a microbiota-based starter culture comprising prokaryotic and eukaryotic components to enhance Cabrales cheese quality. Full article
(This article belongs to the Special Issue Microbiota and Cheese Quality)
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