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Microorganisms
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Food Microbial Diversity 2.0
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Food Microbial Diversity 2.0

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 23667

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

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. 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 2700 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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Related Special Issue

Published Papers (8 papers)

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15 pages, 18849 KiB  
Article
Genomic Analysis and In Vitro Investigation of the Hop Resistance Phenotype of Two Novel Loigolactobacillus backii Strains, Isolated from Spoiled Beer
by Despoina Eugenia Kiousi, Joanna Bucka-Kolendo, Adrian Wojtczak, Barbara Sokołowska, Agapi I. Doulgeraki and Alex Galanis
Microorganisms 2023, 11(2), 280; https://doi.org/10.3390/microorganisms11020280 - 20 Jan 2023
Cited by 7 | Viewed by 1991
Abstract
Loigolactobacillus backii is an important beer-spoiling species, exhibiting high hop tolerance. Here, we present the annotated whole genome sequence of two recently isolated strains, Lg. backii KKP 3565 and KKP 3566. Firstly, to study the genetic basis of the persistence of the two [...] Read more.
Loigolactobacillus backii is an important beer-spoiling species, exhibiting high hop tolerance. Here, we present the annotated whole genome sequence of two recently isolated strains, Lg. backii KKP 3565 and KKP 3566. Firstly, to study the genetic basis of the persistence of the two isolates in beer, a comprehensive bioinformatic analysis ensued. Their chromosome map was constructed, using whole-genome sequencing and assembly, revealing that the two strains carry genomes with a length of 2.79 Mb with a GC content of 40.68%. An average nucleotide identity (ANI) analysis demonstrated that the novel strains possess unique genomic sequences, also confirming their classification into the Lg. backii species. Their genome harbors numerous insertion sequences and plasmids, originating from other beer-spoiling species. Regarding their adaptation in brewery environment, homologous genes that confer resistance to hop were spotted, while the impact of hop bitters and pure beer on bacterial growth was investigated, in vitro. In brief, low hop concentrations were found to induce the proliferation of strains, while a higher concentration negatively affected their growth. Nonetheless, their ability to survive in pure beer indicated their tolerance to high hop concentrations. These results offer insight into the capacity of Lg. backii KKP 3566 and Lg. backii KKP 3566 to tolerate the extreme conditions prevalent in the brewery environment. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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20 pages, 3980 KiB  
Article
The Impact of Different Inoculation Schemes on the Microbiota, Physicochemical and Sensory Characteristics of Greek Kopanisti Cheese throughout Production and Ripening
by Maria Kazou, Alkmini Gavriil, Olga Kalagkatsi, Theodoros Paschos and Effie Tsakalidou
Microorganisms 2023, 11(1), 66; https://doi.org/10.3390/microorganisms11010066 - 26 Dec 2022
Cited by 2 | Viewed by 2749
Abstract
Kopanisti is a Greek PDO cheese, which is traditionally produced by the addition of an amount of over-mature Kopanisti, called Mana Kopanisti, to initiate cheese ripening. The aim of this study was the production of four types of Kopanisti cheese (A–D) using pasteurized [...] Read more.
Kopanisti is a Greek PDO cheese, which is traditionally produced by the addition of an amount of over-mature Kopanisti, called Mana Kopanisti, to initiate cheese ripening. The aim of this study was the production of four types of Kopanisti cheese (A–D) using pasteurized cow milk, and a combination of the following starters/adjuncts in order to test their ability to be used in Kopanisti cheese production: A: Lactococcus lactis subsp. lactis and Lacticaseibacillus paracasei, B: L. lactis and Lc. paracasei/Mana Kopanisti, C: L. lactis and Lc. paracasei/Ligilactobacillus acidipiscis and Loigolactobacillus rennini, D: Lig. acidipiscis and Loig. rennini. Throughout production and ripening, classical microbiological, metataxonomics and physicochemical analyses were employed, while the final products (Day 35) were subjected to sensory analysis as well. Most interestingly, beta-diversity analysis of the metataxonomics data revealed the clusters constructed among the Kopanisti types based on the different inoculation schemes. On day 35, Kopanisti A–C types clustered together due to their similar 16S microbiota, while Kopanisti D was highly differentiated. On the contrary, ITS data clustered Kopanisti B and C together, while Kopanisti A and D were grouped seperately. Finally, based on the sensory evaluation, Kopanisti C appeared to have the most suitable bacteria cocktail for the Kopanisti cheese production. Therefore, not only were the conventional starters used, but also the Lig. acidipiscis and Loig. rennini strains could be used in a standardized Kopanisti cheese production that could lead to final products of high quality and safety. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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25 pages, 3643 KiB  
Article
Molecular and Physiological Diversity of Indigenous Yeasts Isolated from Spontaneously Fermented Wine Wort from Ilfov County, Romania
by Viorica Maria Corbu and Ortansa Csutak
Microorganisms 2023, 11(1), 37; https://doi.org/10.3390/microorganisms11010037 - 22 Dec 2022
Cited by 10 | Viewed by 3609
Abstract
(1) Background: Wine yeast research offers the possibility of isolating new strains with distinct metabolic properties due to the geographical location of the vineyard and the processes used in winemaking. Our study deals with the isolation and identification of six yeasts from spontaneously [...] Read more.
(1) Background: Wine yeast research offers the possibility of isolating new strains with distinct metabolic properties due to the geographical location of the vineyard and the processes used in winemaking. Our study deals with the isolation and identification of six yeasts from spontaneously fermented wine wort from Romania and their characterization as new potential starter culture for traditional beverages, for food industry or biomedicine. (2) Materials and methods: The isolates were identified using conventional taxonomy tests, phenotypic phylogeny analysis (Biolog YT), MALDI-TOF mass spectrometry, PCR-RFLP, and sequencing of the ITS1-5,8S-ITS2 rDNA region. The capacity of the yeasts to grow under thermal, ionic, and osmotic stress was determined. The safe status was confirmed by testing virulence and pathogenicity factors. Assays were performed in order to evaluate the growth inhibition of Candida strains and determine the antimicrobial mechanism of action. (3) Results and discussions: The yeast isolates were identified as belonging to the Metschinikowia, Hanseniaspora, Torulaspora, Pichia, and Saccharomyces genera. All the isolates were able to develop under the tested stress conditions and were confirmed as safe. With the exception of S. cerevisiae CMGB-MS1-1, all the isolates showed good antimicrobial activity based on competition for iron ions or production of killer toxins. (4) Conclusions: The results revealed the resistance of our yeasts to environmental conditions related to industrial and biomedical applications and their high potential as starter cultures and biocontrol agents, respectively. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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18 pages, 2498 KiB  
Article
Environmental Selection Shapes Bacterial Community Composition in Traditionally Fermented Maize-Based Foods from Benin, Tanzania and Zambia
by Maarten de Jong, Anna Y. Alekseeva, Kulwa F. Miraji, Sydney Phiri, Anita R. Linnemann and Sijmen E. Schoustra
Microorganisms 2022, 10(7), 1354; https://doi.org/10.3390/microorganisms10071354 - 5 Jul 2022
Cited by 4 | Viewed by 2035
Abstract
Natural (microbial) communities are complex ecosystems with many interactions and cross-dependencies. Among other factors, selection pressures from the environment are thought to drive the composition and functionality of microbial communities. Fermented foods, when processed using non-industrial methods, harbor such natural microbial communities. In [...] Read more.
Natural (microbial) communities are complex ecosystems with many interactions and cross-dependencies. Among other factors, selection pressures from the environment are thought to drive the composition and functionality of microbial communities. Fermented foods, when processed using non-industrial methods, harbor such natural microbial communities. In non-alcoholic fermented foods the fermenting microbiota is commonly dominated by 4–10 species of bacteria, which make them suitable model systems to study ecosystem assembly and functioning. In this study, we assess the influence of the environment on the composition of microbial communities of traditional fermented products from Africa. We compare differences between microbial communities that are found in similar products but come from different countries, hypothesizing they experience different environmental selection pressures. We analyzed bacterial community composition in 36 samples of various cereal-based fermented foods from Benin, Tanzania and Zambia using 16S rDNA amplicon sequencing. The differential abundance analysis indicates that the bacterial communities of fermented foods from the three countries are dominated by mostly lactic acid bacteria belonging to the genera of Lactobacillus, Weisella and Curvibacter. The samples from Zambia contain the most dissimilar microbial communities in comparison with samples from Benin and Tanzania. We propose this is caused by the relatively low temperature in Zambia, suggesting that indeed environmental selection can shape community composition of fermenting microbes. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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19 pages, 24592 KiB  
Article
Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics
by Konstantinos Papadimitriou, Rania Anastasiou, Marina Georgalaki, Rimi Bounenni, Argiro Paximadaki, Christina Charmpi, Voula Alexandraki, Maria Kazou and Effie Tsakalidou
Microorganisms 2022, 10(5), 1073; https://doi.org/10.3390/microorganisms10051073 - 23 May 2022
Cited by 17 | Viewed by 3429
Abstract
Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal [...] Read more.
Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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25 pages, 1639 KiB  
Article
Mapping the Key Technological and Functional Characteristics of Indigenous Lactic Acid Bacteria Isolated from Greek Traditional Dairy Products
by Christina S. Kamarinou, Olga S. Papadopoulou, Agapi I. Doulgeraki, Chrysoula C. Tassou, Alex Galanis, Nikos G. Chorianopoulos and Anthoula A. Argyri
Microorganisms 2022, 10(2), 246; https://doi.org/10.3390/microorganisms10020246 - 23 Jan 2022
Cited by 14 | Viewed by 4897
Abstract
The aim of the current study was to isolate indigenous lactic acid bacteria (LAB) from traditional Greek cheeses and assess their biochemical, technological, and functional characteristics, so as to develop novel cultures with multi-functional properties. Hence, 109 LAB isolates were recovered from traditional [...] Read more.
The aim of the current study was to isolate indigenous lactic acid bacteria (LAB) from traditional Greek cheeses and assess their biochemical, technological, and functional characteristics, so as to develop novel cultures with multi-functional properties. Hence, 109 LAB isolates were recovered from traditional fresh cheeses and were evaluated in vitro for their gas production; proteolytic, lipolytic, and haemolytic activity; exopolysaccharide production (EPS); enzymatic potential; and ability to grow at 6.5% NaCl and at different pH, temperature, and anaerobic conditions. Consequently, 48 selected isolates were further evaluated for their survival under simulated gastrointestinal tract conditions, partial bile salt hydrolase activity, antibiotic resistance, and antimicrobial activity against pathogens. These isolates were also incorporated as co-cultures in yogurt production to examine their sensory characteristics and their survival in the product. Some prominent isolates that showed favorable technological and functional characteristics (good survival rates at low pH and bile salts, ability to produce β-galactosidase, and EPS) and attributed desirable sensory characteristics to yogurt were Lactococcuslactis (SRX2, SRX3, SRX5, and SMX16), Lactobacillus paracasei SRX10, and Lactiplantibacillusplantarum (FRX7, FB1), while Leuconostoc mesenteroides FMX3 and L. lactis SMX2 showed an anti-listerial activity in vitro. The results of the present study are promising for the production of novel dairy functional products with an enhanced quality and safety. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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12 pages, 12812 KiB  
Article
Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum
by Colin R. Tinsley, Noémie Jacques, Marine Lucas, Cécile Grondin, Jean-Luc Legras and Serge Casaregola
Microorganisms 2022, 10(1), 103; https://doi.org/10.3390/microorganisms10010103 - 4 Jan 2022
Cited by 3 | Viewed by 1748
Abstract
Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five [...] Read more.
Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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11 pages, 271 KiB  
Perspective
The Clash of Microbiomes: From the Food Matrix to the Host Gut
by Despoina Eugenia Kiousi, Nikos Chorianopoulos, Chrysoula C. Tassou and Alex Galanis
Microorganisms 2022, 10(1), 116; https://doi.org/10.3390/microorganisms10010116 - 6 Jan 2022
Cited by 6 | Viewed by 2101
Abstract
Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific [...] Read more.
Food fermentation has led to the improvement of the safety characteristics of raw materials and the production of new foodstuffs with elevated organoleptic characteristics. The empirical observation that these products could have a potential health benefit has garnered the attention of the scientific community. Therefore, several studies have been conducted in animal and human hosts to decipher which of these products may have a beneficial outcome against specific ailments. However, despite the accumulating literature, a relatively small number of products have been authorized as ‘functional foods’ by regulatory bodies. Data inconsistency and lack of in-depth preclinical characterization of functional products could heavily contribute to this issue. Today, the increased availability of omics platforms and bioinformatic algorithms for comprehensive data analysis can aid in the systematic characterization of microbe–microbe, microbe–matrix, and microbe–host interactions, providing useful insights about the maximization of their beneficial effects. The incorporation of these platforms in food science remains a challenge; however, coordinated efforts and interdisciplinary collaboration could push the field toward the dawn of a new era. Full article
(This article belongs to the Special Issue Food Microbial Diversity 2.0)
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