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New Insights in Microbial Diversity of Fermented Foods
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New Insights in Microbial Diversity of Fermented Foods

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 10266

Special Issue Editors

Dr. Vania Patrone

E-Mail Website
Guest Editor
Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
Interests: food microbiology; lactic acid bacteria (LAB); gut microbiota; probiotics; metagenomics; nutrigenomics
Special Issues, Collections and Topics in MDPI journals
Dr. François Bourdichon

E-Mail Website
Guest Editor
Department for Sustainable Food Process, Faculty of Agriculture, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
Interests: food safety; food fermentation; food cultures

Special Issue Information

Dear Colleagues,

Fermented foods represent many food products produced across diverse cultural and geographic backgrounds and consumed worldwide. Microbial consortia associated with such products, including bacteria, fungi, and viruses, are key to the quality and safety of fermented foods, whether they act as fermentation starters or non-starters. While many studies have examined the composition of the microbial communities in fermented foods, in-depth investigations of the microbiomes, microbiota and microbial metabolites are still scarce. This Special Issue highlights research on microbiota structure and function in fermented food products, with a focus on the interaction between microorganisms and raw materials. We seek papers making a significant contribution to uncovering microbial activities and processes that affect the organoleptic, nutritional, and functional characteristics of the final products.

Dr. Vania Patrone
Dr. François Bourdichon
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fermentation
  • microbiome
  • microbiota
  • metabolites
  • food safety
  • food security
  • sensorial attributes
  • health

Published Papers (6 papers)

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Research

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14 pages, 5889 KiB  
Article
Antarctic Soil Yeasts with Fermentative Capacity and Potential for the Wine Industry
by Laura Navarro, Mariona Gil i Cortiella, Ana Gutiérrez-Moraga, Nancy Calisto, Cristina Ubeda and Gino Corsini
Foods 2023, 12(24), 4496; https://doi.org/10.3390/foods12244496 - 16 Dec 2023
Viewed by 767
Abstract
Low fermentation temperatures are usually employed to obtain high-quality wines. This is especially interesting for white wine production since it prevents the loss of volatile compounds and a browning appearance; however, available fermentative yeasts do not usually tolerate low temperatures. Therefore, an interesting [...] Read more.
Low fermentation temperatures are usually employed to obtain high-quality wines. This is especially interesting for white wine production since it prevents the loss of volatile compounds and a browning appearance; however, available fermentative yeasts do not usually tolerate low temperatures. Therefore, an interesting place to find new yeasts with cryotolerance is the Antarctic continent. From soil samples collected in Antarctica, 125 yeasts were isolated, of which 25 exhibited fermentative activity at 10 °C. After a fingerprinting assay, we classified the candidates into nine isotypes and sequenced internal transcribed spacer regions for their identification. These yeasts were identified as part of the Mrakia genus. Sugar and alcohol tolerance tests showed that some of these Antarctic soil yeasts were able to grow up to 9% alcohol, and 25% sugar was reached; however, they exhibited longer latency periods compared to the control Saccharomyces cerevisiae. The optimal growing temperature for the isolated Antarctic yeasts was between 10 °C and 15 °C. A comprehensive analysis of the results obtained showed that the isolates 10M3-1, 4M3-6, and 4B1-35 could be good candidates for fermentation purposes due to their alcohol, sugar tolerance, and growth features. Our results prove that it is possible to isolate fermentative yeasts from Antarctic soil with promising characteristics for their potential use in the wine production industry. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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15 pages, 2374 KiB  
Article
Non-Saccharomyces Yeasts from Organic Vineyards as Spontaneous Fermentation Agents
by Lorena López-Enríquez, Josefina Vila-Crespo, José Manuel Rodríguez-Nogales, Encarnación Fernández-Fernández and Violeta Ruipérez
Foods 2023, 12(19), 3644; https://doi.org/10.3390/foods12193644 - 02 Oct 2023
Cited by 1 | Viewed by 921
Abstract
Currently, non-Saccharomyces yeasts are the subject of interest, among other things, for their contribution to the aromatic complexity of wines. In this study, the characterisation of non-Saccharomyces yeasts was addressed by their isolation during spontaneous fermentations of organic Verdejo grapes, obtaining [...] Read more.
Currently, non-Saccharomyces yeasts are the subject of interest, among other things, for their contribution to the aromatic complexity of wines. In this study, the characterisation of non-Saccharomyces yeasts was addressed by their isolation during spontaneous fermentations of organic Verdejo grapes, obtaining a total of 484 isolates, of which 11% were identified by molecular techniques as non-Saccharomyces yeasts. Fermentative isolates belonging to the species Hanseniaspora meyeri, Hanseniaspora osmophila, Pichia guilliermondii, Pichia kudriavzevii, Torulaspora delbrueckii, and Wickerhamomyces anomalus were analysed. Significant differences were found in the yeast populations established at the different fermentation stages. Interestingly, W. anomalus stood up as a widely distributed species in vineyards, vintages, and fermentation stages. Several of the strains studied stood out for their biotechnological potential in the production of Verdejo wine, showing the presence of relevant enzymatic activity for the release of varietal aromas and the technological improvement of the winemaking process. Three enzymatic activities were found in an important number of isolates, β-glucosidase, protease, and β-lyase, implicated in the positive aromatic impact on this style of white wine. In that sense, all the isolates of W. anomalus presented those activities. T. delbrueckii isolates were highlighted for their significant β-lyase activity. In addition, T. delbrueckii was outlined because of its potential to achieve an elevated fermenting power, as well as the lack of lag phase. The results obtained highlight the importance of maintaining the microbial diversity that contributes to the production of wines with unique and distinctive characteristics of the production region. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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19 pages, 5152 KiB  
Article
Bacterial and Fungal Communities Are Specifically Modulated by the Cocoa Bean Fermentation Method
by Rebecca Ghisolfi, Francesca Bandini, Filippo Vaccari, Gabriele Bellotti, Cristian Bortolini, Vania Patrone, Edoardo Puglisi and Lorenzo Morelli
Foods 2023, 12(10), 2024; https://doi.org/10.3390/foods12102024 - 17 May 2023
Viewed by 1886
Abstract
Cocoa bean fermentation is carried out in different production areas following various methods. This study aimed to assess how the bacterial and fungal communities were affected by box, ground or jute fermentation methods, using high-throughput sequencing (HTS) of phylogenetic amplicons. Moreover, an evaluation [...] Read more.
Cocoa bean fermentation is carried out in different production areas following various methods. This study aimed to assess how the bacterial and fungal communities were affected by box, ground or jute fermentation methods, using high-throughput sequencing (HTS) of phylogenetic amplicons. Moreover, an evaluation of the preferable fermentation method was carried out based on the microbial dynamics observed. Box fermentation resulted in higher bacterial species diversity, while beans processed on the ground had a wider fungal community. Lactobacillus fermentum and Pichia kudriavzevii were observed in all three fermentation methods studied. Moreover, Acetobacter tropicalis dominated box fermentation and Pseudomonas fluorescens abounded in ground-fermented samples. Hanseniaspora opuntiae was the most important yeast in jute and box, while Saccharomyces cerevisiae prevailed in the box and ground fermentation. PICRUST analysis was performed to identify potential interesting pathways. In conclusion, there were noticeable differences between the three different fermentation methods. Due to its limited microbial diversity and the presence of microorganisms that guarantee good fermentation, the box method was found to be preferable. Moreover, the present study allowed us to thoroughly explore the microbiota of differently treated cocoa beans and to better understand the technological processes useful to obtain a standardized end-product. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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24 pages, 999 KiB  
Article
Queijo Serra da Estrela PDO Cheese: Investigation into Its Morpho-Textural Traits, Microbiota, and Volatilome
by Giorgia Rampanti, Ilario Ferrocino, Joanna Harasym, Roberta Foligni, Federica Cardinali, Agnieszka Orkusz, Vesna Milanović, Irene Franciosa, Cristiana Garofalo, Cinzia Mannozzi, Massimo Mozzon, Andrea Osimani and Lucia Aquilanti
Foods 2023, 12(1), 169; https://doi.org/10.3390/foods12010169 - 29 Dec 2022
Cited by 4 | Viewed by 2341
Abstract
Queijo Serra da Estrela is a PDO Portuguese cheese produced through coagulation of raw ewe’s milk using cardoon (Cynara cardunculus L.) flowers. The present research was aimed at depicting an up-to-date and comprehensive overview of the microbiota of Queijo Serra da Estrela [...] Read more.
Queijo Serra da Estrela is a PDO Portuguese cheese produced through coagulation of raw ewe’s milk using cardoon (Cynara cardunculus L.) flowers. The present research was aimed at depicting an up-to-date and comprehensive overview of the microbiota of Queijo Serra da Estrela cheese. To this end, viable counting and metataxonomic analysis were carried out on cheeses sampled from four Portuguese artisan producers. Physico-chemical and morpho-textural analyses were also performed, together with the analysis of volatile organic compounds (VOCs). Finally, non-starter lactic acid bacteria (NSLAB) isolated from the cheeses were characterized for their enzymatic activities using a semi-quantitative method. According to the metataxonomic analysis, Lactococcus lactis and Lactococcus piscium were the species occurring at the highest relative abundance. The isolates collected from the cheeses were assigned to Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus lactis, Levilactobacillus brevis, Latilactobacillus graminis, Leuconostoc mesenteroides, and the Lacticaseibacillus casei group. The enzymatic characterization of these cultures highlighted esterase, aminopeptidase, acid phosphatase, beta-galactosidase, alpha-glucosidase, and beta-glucosidase among the major enzymatic activities. Fungal populations were dominated by Debaryomyces hansenii and Kurtzmaniella zeylanoides; however, species rarely found in cheese (e.g., Candida boidinii, Vishniacozyma victoriae, and Starmerella) were also detected. The volatile compounds characterizing the analyzed cheeses were carboxylic acids and esters, followed by carbonyl compounds and alcohols. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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Review

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33 pages, 2037 KiB  
Review
The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety
by Jasmine S. Ritschard and Markus Schuppler
Foods 2024, 13(2), 214; https://doi.org/10.3390/foods13020214 - 10 Jan 2024
Viewed by 1670
Abstract
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and [...] Read more.
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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23 pages, 1305 KiB  
Review
The Rising Role of Omics and Meta-Omics in Table Olive Research
by Anastasios Tsoungos, Violeta Pemaj, Aleksandra Slavko, John Kapolos, Marina Papadelli and Konstantinos Papadimitriou
Foods 2023, 12(20), 3783; https://doi.org/10.3390/foods12203783 - 15 Oct 2023
Viewed by 1579
Abstract
Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing [...] Read more.
Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives’ intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives’ microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology. Full article
(This article belongs to the Special Issue New Insights in Microbial Diversity of Fermented Foods)
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