Special Issue "Food Microbial Diversity"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 17334

Special Issue Editors

Dr. Agapi I. Doulgeraki
E-Mail Website1 Website2
Guest Editor
Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, Faculty of Foods, Biotechnology and Development, Agricultural University of Athens (AUA), Iera Odos 75, 11855 Athens, Greece
Interests: food microbiota; molecular microbiology; active packaging; biofilm formation and decontamination; probiotic bacteria; gene expression
Special Issues, Collections and Topics in MDPI journals
Dr. Chrysoula Tassou
E-Mail Website
Guest Editor
Hellenic Agricultural Organisation-DEMETER, Institute of Technology of Agricultural Products, Sofokli Venizelou 1, Lycovrissi, 14123 Attica, Greece
Interests: food microbiology; food safety; probiotics; microbiology of fermented foods; food microbial ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The study of microbial diversity of foods is essential to understand the quality and safety aspects of a type of food. Through the years, different approaches have been adopted to monitor and characterize the microorganisms present in a certain type of food. Beyond microbial enumeration on selective media, isolation of microorganisms from a food matrix was essential to identify the food microbiota. In this case, microbial characterization was performed through the application of morphological and biochemical tests and/or molecular approaches. However, the evolution of molecular biology has led to the development of new technologies where the DNA is extracted directly from a sample and the microbiota could be analyzed by analyzing the massive sequences resulting from these methods. In recent years, these technologies have been adopted by food scientists and have been applied to map the microorganisms present in a particular type of food.

This Special Issue of Microorganisms aims to collect the latest articles that examine the microbial diversity of foods, e.g., raw, processed, fermented foods. We invite contributions as original research articles or reviews that cover any aspect of food microbial diversity. We encourage researchers to submit their works using culture-dependent and culture-independent techniques applied for microbiome characterization, as well as an exploration of microbial physiology and properties. We are especially interested in research works aiming to identify the microbial diversity of foods and their impact on food safety and quality aspects.

Dr. Agapi I. Doulgeraki
Dr. Chrysoula Tassou
Guest Editors

Manuscript Submission Information

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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. Microorganisms is an international peer-reviewed open access monthly 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 2200 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

food microbiota
microbial diversity
omic technologies
microbial characterization
culture-dependent methods
culture-independent methods

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Published Papers (9 papers)

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Editorial

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Editorial
Food Microbial Diversity
Microorganisms 2021, 9(12), 2556; https://doi.org/10.3390/microorganisms9122556 - 10 Dec 2021
Viewed by 638
Abstract
The microbiological quality and safety of food could be assessed by mapping the microorganisms present in a particular type of food [...] Full article
(This article belongs to the Special Issue Food Microbial Diversity)

Research

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Article
Mycobiota in the Carposphere of Sour and Sweet Cherries and Antagonistic Features of Potential Biocontrol Yeasts
Microorganisms 2021, 9(7), 1423; https://doi.org/10.3390/microorganisms9071423 - 30 Jun 2021
Cited by 4 | Viewed by 1143
Abstract
Sour cherries (Prunus cerasus L.) and sweet cherries (P. avium L.) are economically important fruits with high potential in the food industry and medicine. In this study, we analyzed fungal communities associated with the carposphere of sour and sweet cherries that [...] Read more.
Sour cherries (Prunus cerasus L.) and sweet cherries (P. avium L.) are economically important fruits with high potential in the food industry and medicine. In this study, we analyzed fungal communities associated with the carposphere of sour and sweet cherries that were freshly harvested from private plantations and purchased in a food store. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput NGS sequencing. Analysis of 168,933 high-quality reads showed the presence of 690 fungal taxa. Investigation of microbial ASVs diversity revealed plant-dependent and postharvest handling-affected fungal assemblages. Among the microorganisms inhabiting tested berries, potentially beneficial or pathogenic fungi were documented. Numerous cultivable yeasts were isolated from the surface of tested berries and characterized by their antagonistic activity. Some of the isolates, identified as Aureobasidium pullulans, Metschnikowia fructicola, and M. pulcherrima, displayed pronounced activity against potential fungal pathogens and showed attractiveness for disease control. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
Microorganisms 2021, 9(5), 1060; https://doi.org/10.3390/microorganisms9051060 - 14 May 2021
Cited by 14 | Viewed by 4135
Abstract
Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of [...] Read more.
Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Assessing the Biofilm Formation Capacity of the Wine Spoilage Yeast Brettanomyces bruxellensis through FTIR Spectroscopy
Microorganisms 2021, 9(3), 587; https://doi.org/10.3390/microorganisms9030587 - 12 Mar 2021
Cited by 2 | Viewed by 1631
Abstract
Brettanomyces bruxellensis is a wine spoilage yeast known to colonize and persist in production cellars. However, knowledge on the biofilm formation capacity of B. bruxellensis remains limited. The present study investigated the biofilm formation of 11 B. bruxellensis strains on stainless steel coupons [...] Read more.
Brettanomyces bruxellensis is a wine spoilage yeast known to colonize and persist in production cellars. However, knowledge on the biofilm formation capacity of B. bruxellensis remains limited. The present study investigated the biofilm formation of 11 B. bruxellensis strains on stainless steel coupons after 3 h of incubation in an aqueous solution. FTIR analysis was performed for both planktonic and attached cells, while comparison of the obtained spectra revealed chemical groups implicated in the biofilm formation process. The increased region corresponding to polysaccharides and lipids clearly discriminated the obtained spectra, while the absorption peaks at the specific wavenumbers possibly reveal the presence of β-glucans, mannas and ergosterol. Unsupervised clustering and supervised classification were employed to identify the important wavenumbers of the whole spectra. The fact that all the metabolic fingerprints of the attached versus the planktonic cells were similar within the same cell phenotype class and different between the two phenotypes, implies a clear separation of the cell phenotype; supported by the results of the developed classification model. This study represents the first to succeed at applying a non-invasive technique to reveal the metabolic fingerprint implicated in the biofilm formation capacity of B. bruxellensis, underlying the homogenous mechanism within the yeast species. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa
Microorganisms 2021, 9(3), 507; https://doi.org/10.3390/microorganisms9030507 - 27 Feb 2021
Cited by 9 | Viewed by 1751
Abstract
Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard [...] Read more.
Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Microbial Diversity of Fermented Greek Table Olives of Halkidiki and Konservolia Varieties from Different Regions as Revealed by Metagenomic Analysis
Microorganisms 2020, 8(8), 1241; https://doi.org/10.3390/microorganisms8081241 - 14 Aug 2020
Cited by 11 | Viewed by 2391
Abstract
Current information from conventional microbiological methods on the microbial diversity of table olives is insufficient. Next-generation sequencing (NGS) technologies allow comprehensive analysis of their microbial community, providing microbial identity of table olive varieties and their designation of origin. The purpose of this study [...] Read more.
Current information from conventional microbiological methods on the microbial diversity of table olives is insufficient. Next-generation sequencing (NGS) technologies allow comprehensive analysis of their microbial community, providing microbial identity of table olive varieties and their designation of origin. The purpose of this study was to evaluate the bacterial and yeast diversity of fermented olives of two main Greek varieties collected from different regions—green olives, cv. Halkidiki, from Kavala and Halkidiki and black olives, cv. Konservolia, from Magnesia and Fthiotida—via conventional microbiological methods and NGS. Total viable counts (TVC), lactic acid bacteria (LAB), yeast and molds, and Enterobacteriaceae were enumerated. Microbial genomic DNA was directly extracted from the olives’ surface and subjected to NGS for the identification of bacteria and yeast communities. Lactobacillaceae was the most abundant family in all samples. In relation to yeast diversity, Phaffomycetaceae was the most abundant yeast family in Konservolia olives from the Magnesia region, while Pichiaceae dominated the yeast microbiota in Konservolia olives from Fthiotida and in Halkidiki olives from both regions. Further analysis of the data employing multivariate analysis allowed for the first time the discrimination of cv. Konservolia and cv. Halkidiki table olives according to their geographical origin. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Characterization of Indigenous Lactic Acid Bacteria in Cow Milk of the Maltese Islands: A Geographical and Seasonal Assessment
Microorganisms 2020, 8(6), 812; https://doi.org/10.3390/microorganisms8060812 - 28 May 2020
Cited by 6 | Viewed by 1208
Abstract
A geographical and seasonal assessment of indigenous lactic acid bacteria (LAB) in Maltese cow milk was conducted in this study. To investigate this, milk was collected from different regions of Malta during winter and summer seasons. Total viable counts (TVC) and LAB population [...] Read more.
A geographical and seasonal assessment of indigenous lactic acid bacteria (LAB) in Maltese cow milk was conducted in this study. To investigate this, milk was collected from different regions of Malta during winter and summer seasons. Total viable counts (TVC) and LAB population were enumerated. Afterwards, LAB were isolated and identified by molecular methods. According to the results, similar TVC were enumerated on winter and summer samples, while highest LAB population was detected on summer samples. LAB isolates were grouped in seven different clusters which were assigned to Lactobacillus casei, Pediococcus pentosaceus, Lactobacillus plantarum, Weissella paramesenteroides, Lactobacillus rhamnosus, Lactococcus lactis, and Lactococcus garvieae. In addition, Enterococcus and Streptococcus species were also isolated. Season seemed to affect the genus/species of LAB since Lactobacillus were mainly isolated from winter samples, while Lactococcus and Enterococcus species were the main genera identified in summer samples. Regarding the geographical distribution, the majority of the Lactobacillus spp. were isolated from the South-eastern region in both seasons. In conclusion, through this study the diversity of indigenous LAB in the Maltese cow milk was monitored for the first time and highlighted that the microbial communities are affected by seasonality and geographical distribution of the farms. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis
Microorganisms 2020, 8(5), 672; https://doi.org/10.3390/microorganisms8050672 - 06 May 2020
Cited by 15 | Viewed by 1986
Abstract
Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this [...] Read more.
Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Review

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Review
Understanding Wine through Yeast Interactions
Microorganisms 2021, 9(8), 1620; https://doi.org/10.3390/microorganisms9081620 - 29 Jul 2021
Cited by 9 | Viewed by 1314
Abstract
Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast [...] Read more.
Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast interactions occur even from the early stages of fermentation, determining yeast community structure and dynamics during the process. Different types of microbial interactions (e.g., mutualism and commensalism or competition and amensalism) may exert positive or negative effects, respectively, on yeast populations. Interactions are intimately linked to yeast metabolic activities that influence the wine analytical profile and shape the wine character. In this context, much attention has been given during the last years to the interactions between Saccharomyces cerevisiae (SC) and non-Saccharomyces (NS) yeast species with respect to their metabolic contribution to wine quality. Yet, there is still a significant lack of knowledge on the interaction mechanisms modulating yeast behavior during mixed culture fermentation, while much less is known about the interactions between the various NS species or between SC and Saccharomyces non-cerevisiae (SNC) yeasts. There is still much to learn about their metabolic footprints and the genetic mechanisms that alter yeast community equilibrium in favor of one species or another. Gaining deeper insights on yeast interactions in the grape–wine ecosystem sets the grounds for understanding the rules underlying the function of the wine microbial system and provides means to better control and improve oenological practices. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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