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: 31 May 2026 | Viewed by 4453

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
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. Área de Tecnología de los Alimentos, Facultad de Ciencias, Universidad de Vigo, Campus Universitario, s/n, 32004 Ourense, Spain
2. Instituto de Agroecoloxía e Alimentación (IAA), Universidade de Vigo, Campus Auga, 32004 Ourense, Spain
Interests: food quality; functional foods; fermented foods; meat products; meat product innovation; dairy products; cheese ripening
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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 (4 papers)

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Research

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19 pages, 1115 KB  
Article
Use of Ligilactobacillus salivarius SP36 as an Adjunct Culture by an Artisan Dairy and Isolation of New Autochthonous Strains with Technological Potential for Cheesemaking
by Josué Jara, Claudio Alba, Javier Calzada, Lucía Largo, Marta Kellermann, Sara Rosado, Marta Ávila, Sonia Garde and Juan M. Rodríguez
Foods 2026, 15(8), 1362; https://doi.org/10.3390/foods15081362 - 14 Apr 2026
Viewed by 451
Abstract
Artisanal cheese quality relies on a complex microbiota. The generalized use of commercial starter cultures has been associated with reduced microbial diversity, fueling interest in using indigenous lactic acid bacteria (LAB) as adjunct cultures. This study aimed to evaluate Ligilactobacillus salivarius SP36 as [...] Read more.
Artisanal cheese quality relies on a complex microbiota. The generalized use of commercial starter cultures has been associated with reduced microbial diversity, fueling interest in using indigenous lactic acid bacteria (LAB) as adjunct cultures. This study aimed to evaluate Ligilactobacillus salivarius SP36 as a starter or adjunct culture in ripened cheeses. Culture-based and culture-independent analyses were performed, together with the assessment of some physico-chemical parameters (pH, water activity, and color), including the profile of volatile compounds. All cheeses were microbiologically safe according to current EU legislation. The pH of the cheese made only with the SP36 strain was higher than those of the cheeses manufactured with a commercial starter (with or without strain SP36). L. salivarius SP36 modulated the aroma profile by increasing ethyl esters, alcohols, ketones, organic acids and sulphur compounds. LAB dominated all cheeses, with the highest microbial diversity in the cheese produced without the commercial starter. Lactiplantibacillus plantarum and Lacticaseibacillus paracasei isolates were obtained from all cheeses. Overall, L. salivarius SP36 seems a promising adjunct for mature cheeses, while autochthonous L. plantarum and L. paracasei isolates represent promising candidates for starter or adjunct cultures. Full article
(This article belongs to the Special Issue Microbiota and Cheese Quality)
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17 pages, 930 KB  
Article
Microbiological Quality of Spanish Aged Cheeses and the Antimicrobial Resistance Profiles of Associated Enterococci, Staphylococci and Enterobacterales
by Celia Arraiz-Fernandez, Alba Martinez-Laorden, Gonzalo Ibañez-Torija and Elena Gonzalez-Fandos
Foods 2026, 15(4), 721; https://doi.org/10.3390/foods15040721 - 15 Feb 2026
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Abstract
The aim of this work was to evaluate the microbiological quality of Spanish aged cheeses and the antimicrobial resistance of enterococci, staphylococci and Enterobacterales. A total of 60 aged cheeses produced in northern Spain were collected at the retail level. Mesophiles, lactic [...] Read more.
The aim of this work was to evaluate the microbiological quality of Spanish aged cheeses and the antimicrobial resistance of enterococci, staphylococci and Enterobacterales. A total of 60 aged cheeses produced in northern Spain were collected at the retail level. Mesophiles, lactic acid bacteria, staphylococci, enterococci, Enterobacterales, and yeast counts were determined. More microbial diversity was found in raw milk cheeses than in those elaborated with pasteurized milk. In general, lactic acid bacteria were the dominant microorganism, mainly Lactiplantibacillus lactis. High resistance rates were observed in E. faecalis strains isolated from raw milk cheeses (74.42%), being 9.30% multi-resistant. The dominant staphylococci found was Staphylococcus equorum. Multi-resistant S. equorum strains were isolated both from raw (1.69%) and pasteurized milk cheeses (9.09%). Hafnia alvei was the predominant bacterium in raw milk cheeses. Fifteen Enterobacterales strains, isolated from raw milk cheeses, showed multi-resistance (37.5%), and seven strains were ESBL producers (17.5%). Escherichia coli was only isolated from 5. 56% of raw milk cheeses, but all of them were extended-espectrum B-lactamase (ESBL) producers. The dominant yeast was D. hansenni, followed by Kluyveromyces lactis. Full article
(This article belongs to the Special Issue Microbiota and Cheese Quality)
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20 pages, 1381 KB  
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
Cited by 1 | Viewed by 1030
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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Review

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37 pages, 748 KB  
Review
Clarifying the Dual Role of Staphylococcus spp. in Cheese Production
by Alessandra Casagrande Ribeiro, Déborah Tavares Alves, Gabriela Zampieri Campos, Talita Gomes da Costa, Bernadette Dora Gombossy de Melo Franco, Felipe Alves de Almeida and Uelinton Manoel Pinto
Foods 2025, 14(22), 3823; https://doi.org/10.3390/foods14223823 - 7 Nov 2025
Viewed by 1960
Abstract
Staphylococcus spp. present a dual role in cheese production as some species are pathogenic, while others bring beneficial characteristics. Coagulase-positive staphylococci (CoPS), particularly Staphylococcus aureus, are of concern due to their ability to produce enterotoxins linked to foodborne outbreaks. These toxins, encoded [...] Read more.
Staphylococcus spp. present a dual role in cheese production as some species are pathogenic, while others bring beneficial characteristics. Coagulase-positive staphylococci (CoPS), particularly Staphylococcus aureus, are of concern due to their ability to produce enterotoxins linked to foodborne outbreaks. These toxins, encoded by staphylococcal enterotoxin (SE) genes, cause gastroenteritis, especially vomiting. Many members of the genus harbor a plethora of virulence genes and are able to form biofilms. The prevalence of antibiotic-resistant strains, including methicillin-resistant S. aureus (MRSA), complicates control. In contrast, some members of the coagulase-negative staphylococci (CoNS) group, such as Staphylococcus carnosus, Staphylococcus condimenti, Staphylococcus equorum, Staphylococcus piscifermentans, Staphylococcus succinus, and Staphylococcus xylosus, contribute to ripening, influencing flavor and texture. Some are even considered safe and studied for their ability to inhibit pathogens. Expression of enterotoxin genes in Staphylococcus, particularly S. aureus, is influenced by environmental factors and can be regulated by different mechanisms including quorum sensing. Understanding gene expression in conditions found during cheese production and ripening can help in formulating effective interventions. Risks posed by enterotoxin-producing Staphylococcus in cheese are evident, with numerous outbreaks reported worldwide. Moreover, several species present risks to both animal and human health. Effective control measures include adherence to microbiological criteria in foods, animal health monitoring, good manufacturing practices (GMP), temperature control, proper ripening conditions and hygiene. This review compiles and discusses existing knowledge on CoPS and CoNS in cheeses, providing a framework for evaluating their risks and benefits and guiding future studies in cheese microbiology. Full article
(This article belongs to the Special Issue Microbiota and Cheese Quality)
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