Screening and Characterization of the Diversity of Food Microorganisms and Their Metabolites

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 46111

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Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Department of Chemical Engineering (DEQ), Faculty of Engineering, University of Porto (FEUP), Porto, Portugal
Interests: food microbiota; chromatography and mass spectrometry; separation processes; valorisation of agro-food by-products; fermentation processes and microbial starter cultures; sourdough and breadmaking
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Department of Biological Engineering, School of Engineering, University of Minho, 4704-553 Braga, Portugal
Interests: industrial and food biotechnology; fermentation processes; food processing; agro-industry by-products valorization; prebiotics production
Special Issues, Collections and Topics in MDPI journals

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Institute of Functional Biology and Genomics (IBFG), Salamanca, Spain
Interests: yeasts genetics and molecular biology; industrial yeasts; new starters for bread and wine making; yeast hybrids; microbiomes of fermented doughs, vineyards and wines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This is a comprehensive Special Issue covering virtually all scientific lines of food microbiology. Topics include the prospection of microbial species in food and feed matrixes and their genotypic and phenotypic characterization, the contribution of beneficial strains, innovative fermentation and technological procedures towards nutritional and health attributes of food, and the exploitation of microbial metabolites.

Culture-dependent and independent techniques for systematic analyses of bacterial and fungal microbiomes are to be considered. The screening and characterization of food spoilage microorganisms, and its potential risks and effects on consumers is another subject to be included in this Special Issue. Topics related to the role of fermentation and the potential of encrypted phenotypic traits of microorganisms towards food hygiene, safety, and resistance to microbial spoilage are welcome. The elucidation of microbial dynamics and relationships with biotic and abiotic factors are of interest. The contribution of beneficial microorganisms, starter cultures, and innovative fermentation and processing technologies to the nutritional, technological, and health attributes of food should be highlighted in this Special Issue. The identification, characterization, and production of functional microbial substances during fermentation or by elected microorganisms will be highly relevant to designing breakthrough metabolites for food, feed, nutraceutical, cosmetic and pharmaceutical industries, and the elucidation of the corresponding metabolic pathways and optimal growth conditions.

Dr. João Miguel F. Rocha
Prof. José António Teixeira
Dr. Mercedes Tamame
Guest Editors

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Published Papers (9 papers)

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Research

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18 pages, 1648 KiB  
Article
Electrochemical Determination of Antioxidant Capacity of Traditional Homemade Fruit Vinegars Produced with Double Spontaneous Fermentation
by Maja Chochevska, Elizabeta Jančovska Seniceva, Sanja Kostadinović Veličkovska, Galaba Naumova-Leţia, Valentin Mirčeski, João Miguel F. Rocha and Tuba Esatbeyoglu
Microorganisms 2021, 9(9), 1946; https://doi.org/10.3390/microorganisms9091946 - 13 Sep 2021
Cited by 8 | Viewed by 2740
Abstract
In the current study, the antioxidant activity of traditional homemade fruit vinegars (HMV) was estimated by measuring the rate of homogeneous redox reaction with 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical cation (ABTS•+) using cyclic voltammetry. The antioxidant capacity of six HMV produced using traditional [...] Read more.
In the current study, the antioxidant activity of traditional homemade fruit vinegars (HMV) was estimated by measuring the rate of homogeneous redox reaction with 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical cation (ABTS•+) using cyclic voltammetry. The antioxidant capacity of six HMV produced using traditional methods and the physicochemical characterization were measured in different vinegar production steps throughout a double spontaneous fermentation process, i.e., without any addition of yeasts or acetic acid bacteria. Their antioxidant capacity was compared with seven fruit commercial vinegars (ComV). Furthermore, the antioxidant capacity was independently measured with the TEAC (Trolox equivalent antioxidant capacity) assay, aiming at correlating with the electrochemical experimental data. Obtained results from both methods, the electrochemical and TEAC assays, interestingly indicated that all HMV have at least 10 times higher antioxidant activity than ComV. Furthermore, the large range of values for antioxidant capacity in samples of commercial vinegars from apples attested the importance of the raw material quality and technological procedures. The positive correlation between total phenolic content and antioxidant capacity measured by the two type of assays indicated that rose hip homemade vinegar (HMV5) has the highest antioxidant capacity. In contrast, the lowest levels of phenolic compounds and antioxidant capacity were found in apple and persimmon homemade vinegars (HMV1 and HMV6, respectively) which indicated that the type of fruit is crucial towards the production of high-quality vinegars. In this way, the use of traditional processes for the production of fruit vinegars proved to be very promising in terms of producing differentiated vinegars and, concomitantly, reaching high levels of health-promoting antioxidant capacities. Full article
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15 pages, 309 KiB  
Article
Multiple Techno-Functional Characteristics of Leuconostoc and Their Potential in Sourdough Fermentations
by Denise C. Müller, Sandra Mischler, Regine Schönlechner and Susanne Miescher Schwenninger
Microorganisms 2021, 9(8), 1633; https://doi.org/10.3390/microorganisms9081633 - 30 Jul 2021
Cited by 8 | Viewed by 2169
Abstract
In this study, the potential of Leuconostoc as non-conventional sourdough starter cultures was investigated. A screening for antifungal activities of 99 lactic acid bacteria (LAB) strains revealed high suppression of bakery-relevant moulds in nine strains of Leuconostoc with activities against Penicillium sp., Aspergillus [...] Read more.
In this study, the potential of Leuconostoc as non-conventional sourdough starter cultures was investigated. A screening for antifungal activities of 99 lactic acid bacteria (LAB) strains revealed high suppression of bakery-relevant moulds in nine strains of Leuconostoc with activities against Penicillium sp., Aspergillus sp., and Cladosporium sp. Mannitol production was determined in 49 Leuconostoc strains with >30 g/L mannitol in fructose (50 g/L)-enriched MRS. Further, exopolysaccharides (EPS) production was qualitatively determined on sucrose (40 g/L)-enriched MRS agar and revealed 59 EPS positive Leuconostoc strains that harboured dextransucrase genes, as confirmed by PCR. Four multifunctional Lc. citreum strains (DCM49, DCM65, MA079, and MA113) were finally applied in lab-scale sourdough fermentations (30 °C, 24 h). Lc. citreum was confirmed by MALDI-TOF MS up to 9 log CFU/g and pH dropped to 4.0 and TTA increased to 12.4. Antifungal compounds such as acetic acid, phenyllactic and hydroxyphenyllactic acids were determined up to 1.7 mg/g, 2.1 µg/g, and 1.3 µg/g, respectively, mannitol up to 8.6 mg/g, and EPS up to 0.62 g/100 g. Due to the observed multifunctionalities and the competitiveness in the natural flour microbiota present in sourdoughs, non-conventional LAB genera such as Leuconostoc seem promising for application in sourdough-based bakery products. Full article
18 pages, 1188 KiB  
Article
Isolation and Characterization of Lactic Acid Bacteria and Yeasts from Typical Bulgarian Sourdoughs
by Mariana Petkova, Petya Stefanova, Velitchka Gotcheva and Angel Angelov
Microorganisms 2021, 9(7), 1346; https://doi.org/10.3390/microorganisms9071346 - 22 Jun 2021
Cited by 18 | Viewed by 4236
Abstract
Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such [...] Read more.
Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such cultures is based on geographical specificity and beneficial technological properties. In this connection, the aim of this study was to isolate, identify and characterize lactic acid bacteria (LAB) and yeasts from typical Bulgarian sourdoughs for the selection of strains for commercial sourdough starter cultures. Twelve samples of typical Bulgarian sourdoughs were collected from different geographical locations. All samples were analyzed for pH, total titratable acidity and dry matter content. Enumeration of LAB and yeast was also carried out. Molecular identification by 16S rDNA sequence analysis was performed for 167 LAB isolates, and 106 yeast strains were identified by ITS1-5.8S-ITS2 rRNA gene partial sequence analysis. The LAB strains were characterized according to their amylolytic and proteolytic activity and acidification capacity, and 11 strains were selected for further testing of their antimicrobial properties. The strains with the most pronounced antibacterial and antifungal activity are listed as recommended candidates for the development of starter cultures for sourdoughs or other food products. Full article
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17 pages, 1494 KiB  
Article
Insights into the Potential of Sourdough-Related Lactic Acid Bacteria to Degrade Proteins in Wheat
by Vera Fraberger, Martin Ladurner, Alexandra Nemec, Clemens Grunwald-Gruber, Lisa M. Call, Rupert Hochegger, Konrad J. Domig and Stefano D’Amico
Microorganisms 2020, 8(11), 1689; https://doi.org/10.3390/microorganisms8111689 - 30 Oct 2020
Cited by 22 | Viewed by 3448
Abstract
Sourdough processing contributes to better digestible wheat-based bakery products, especially due to the proteolytic activity of lactic acid bacteria (LAB). Therefore, sourdough-related LAB were screened for their capacity to degrade immunogenic proteins like gluten and alpha-amylase-trypsin inhibitors (ATIs). Firstly, the growth of 87 [...] Read more.
Sourdough processing contributes to better digestible wheat-based bakery products, especially due to the proteolytic activity of lactic acid bacteria (LAB). Therefore, sourdough-related LAB were screened for their capacity to degrade immunogenic proteins like gluten and alpha-amylase-trypsin inhibitors (ATIs). Firstly, the growth of 87 isolates was evaluated on a gluten-based medium. Further, the breakdown capacity of selected isolates was determined for gluten with a focus on gliadins by measuring acidification parameters and MALDI-TOF MS protein profiles. ATI degradation after 72 h of incubation within an ATI-based medium was investigated by means of acidification, HPLC, and competitive ELISA. All isolates exhibited the potential to degrade ATIs to a high degree, whereas the gliadin degradation capacity varied more greatly among tested LAB, with Lacticaseibacillus paracasei Lpa4 exhibiting the strongest alterations of the gliadin pattern, followed by Lactiplantibacillus plantarum Lpl5. ATI degradation capacities ranged from 52.3% to 85.0% by HPLC and 22.2% to 70.2% by ELISA, with Lacticaseibacillus paracasei Lpa4 showing superior breakdown properties. Hence, a selection of specific starter cultures can be used in sourdough processing for wheat-based bakery products with reduced gluten and ATI content and, further, better tolerated products for patients suffering from non-celiac wheat sensitivity (NCWS). Full article
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22 pages, 4421 KiB  
Article
Pepper Bacterial Spot Control by Bacillus velezensis: Bioprocess Solution
by Ivana Pajčin, Vanja Vlajkov, Marcus Frohme, Sergii Grebinyk, Mila Grahovac, Marija Mojićević and Jovana Grahovac
Microorganisms 2020, 8(10), 1463; https://doi.org/10.3390/microorganisms8101463 - 24 Sep 2020
Cited by 26 | Viewed by 4307
Abstract
Pepper bacterial spot is one of the most severe plant diseases in terms of infection persistence and economic losses when it comes to fresh pepper fruits used in nutrition and industrial processing. In this study, Bacillus velezensis IP22 isolated from fresh cheese was [...] Read more.
Pepper bacterial spot is one of the most severe plant diseases in terms of infection persistence and economic losses when it comes to fresh pepper fruits used in nutrition and industrial processing. In this study, Bacillus velezensis IP22 isolated from fresh cheese was used as a biocontrol agent of pepper bacterial spot, whose main causal agent is the cosmopolitan pathogen Xanthomonas euvesicatoria. After optimization of the cultivation medium composition aimed at maximizing of the antimicrobial activity against X. euvesicatoria and validation of the optimized medium at the scale of a laboratory bioreactor, in planta tests were performed. The results have showed significant suppression of bacterial spot symptoms in pepper plants by the produced biocontrol agent, as well as reduction of disease spreading on the healthy (uninoculated) pepper leaves. Furthermore, HPLC-MS (high pressure liquid chromatography–mass spectrometry) analysis was employed to examine antimicrobial metabolites produced by B. velezensis IP22, where lipopeptides were found with similar m/z values compared to lipopeptides from fengycin and locillomycin families. The bioprocess solution developed at the laboratory scale investigated in this study represents a promising strategy for production of pepper bacterial spot biocontrol agent based on B. velezensis IP22, a food isolate with a great perspective for application in plant protection. Full article
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26 pages, 1312 KiB  
Article
Bioconversion of Milk Permeate with Selected Lactic Acid Bacteria Strains and Apple By-Products into Beverages with Antimicrobial Properties and Enriched with Galactooligosaccharides
by Egle Zokaityte, Darius Cernauskas, Dovile Klupsaite, Vita Lele, Vytaute Starkute, Paulina Zavistanaviciute, Modestas Ruzauskas, Romas Gruzauskas, Grazina Juodeikiene, João Miguel Rocha, Saulius Bliznikas, Pranas Viskelis, Romas Ruibys and Elena Bartkiene
Microorganisms 2020, 8(8), 1182; https://doi.org/10.3390/microorganisms8081182 - 3 Aug 2020
Cited by 40 | Viewed by 3870
Abstract
The present research study aims to prepare prototypes of beverages from milk permeate (MP) using fermentation with 10 different strains of lactic acid bacteria (LAB) showing antimicrobial properties (L. uvarum LUHS245, L. casei LUHS210, L. curvatus LUHS51, L. plantarum LUHS135, P. [...] Read more.
The present research study aims to prepare prototypes of beverages from milk permeate (MP) using fermentation with 10 different strains of lactic acid bacteria (LAB) showing antimicrobial properties (L. uvarum LUHS245, L. casei LUHS210, L. curvatus LUHS51, L. plantarum LUHS135, P. acidilactici LUHS29, L. plantarum LUHS122, L. coryniformins LUHS71, L. paracasei LUHS244, P. pentosaceus LUHS183, L. faraginis LUHS206) and MP with (AppMP) or without (MP) the addition of 8% (w/w) apple by-products (App). Two groups of prototypes of beverages were prepared: fermented MP and fermented MP with App (AppMP). Acidity parameters, LAB viable counts, lactose and galactooligosaccharides (GOSs) content, antimicrobial properties against 15 pathogenic and opportunistic bacterial strains, overall acceptability and emotions induced of the final fermented beverages for consumers were evaluated. Results showed that all LAB grew well in MP and LAB strain exhibited a significant (p ≤ 0.05) influence on galactobiose and galactotriose synthesis in the fermentable MP substrate. The highest total content of GOS (26.80 mg/100 mL) was found in MPLUHS29 fermented beverage. In addition, MPLUHS245, MPLUHS210 and AppMPLUHS71 fermented beverages showed high antimicrobial activity, inhibiting 13 out of 15 tested microbial pathogens. The overall acceptability of AppMP fermented beverages was 26.8% higher when compared with fermented beverages without App (MP), and the most intensive “happy” emotion was induced by MPLUHS71, MPLUHS24, MPLUHS183 and MPLUHS206 samples. Finally, very promising results were also attained by the bioconversion of MP with selected LAB and App addition into the prototypes of antimicrobial beverages enriched with GOS. Full article
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22 pages, 3191 KiB  
Article
New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses
by Simon Begrem, Flora Ivaniuk, Frédérique Gigout-Chevalier, Laetitia Kolypczuk, Sandrine Bonnetot, Françoise Leroi, Olivier Grovel, Christine Delbarre-Ladrat and Delphine Passerini
Microorganisms 2020, 8(7), 1093; https://doi.org/10.3390/microorganisms8071093 - 21 Jul 2020
Cited by 11 | Viewed by 3153
Abstract
Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with [...] Read more.
Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications. Full article
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Review

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24 pages, 934 KiB  
Review
Sourdough Microbiome Comparison and Benefits
by Siew Wen Lau, Ann Qi Chong, Nyuk Ling Chin, Rosnita A. Talib and Roseliza Kadir Basha
Microorganisms 2021, 9(7), 1355; https://doi.org/10.3390/microorganisms9071355 - 23 Jun 2021
Cited by 40 | Viewed by 14431
Abstract
Sourdough is the oldest form of leavened bread used as early as 2000 BC by the ancient Egyptians. It may have been discovered by accident when wild yeast drifted into dough that had been left out resulting in fermentation of good microorganisms, which [...] Read more.
Sourdough is the oldest form of leavened bread used as early as 2000 BC by the ancient Egyptians. It may have been discovered by accident when wild yeast drifted into dough that had been left out resulting in fermentation of good microorganisms, which made bread with better flavour and texture. The discovery was continued where sourdough was produced as a means of reducing wastage with little known (at that point of time) beneficial effects to health. With the progress and advent of science and technology in nutrition, sourdough fermentation is now known to possess many desirable attributes in terms of health benefits. It has become the focus of attention and practice in modern healthy eating lifestyles when linked to the secret of good health. The sourdough starter is an excellent habitat where natural and wild yeast plus beneficial bacteria grow by ingesting only water and flour. As each sourdough starter is unique, with different activities, populations and interactions of yeast and bacteria due to different ingredients, environment, fermentation time and its carbohydrate fermentation pattern, there is no exact elucidation on the complete make-up of the sourdough microbiome. Some lactic acid bacteria (LAB) strains that are part of the sourdough starter are considered as probiotics which have great potential for improving gastrointestinal health. Hence, from a wide literature surveyed, this paper gives an overview of microbial communities found in different sourdough starters. This review also provides a systematic analysis that identifies, categorises and compares these microbes in the effort of linking them to specific functions, particularly to unlock their health benefits. Full article
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21 pages, 1462 KiB  
Review
Traditional Bulgarian Dairy Products: Ethnic Foods with Health Benefits
by Penka Petrova, Ivan Ivanov, Lidia Tsigoriyna, Nadezhda Valcheva, Evgenia Vasileva, Tsvetomila Parvanova-Mancheva, Alexander Arsov and Kaloyan Petrov
Microorganisms 2021, 9(3), 480; https://doi.org/10.3390/microorganisms9030480 - 25 Feb 2021
Cited by 27 | Viewed by 6023
Abstract
The reported health effects of fermented dairy foods, which are traditionally manufactured in Bulgaria, are connected with their microbial biodiversity. The screening and development of probiotic starters for dairy products with unique properties are based exclusively on the isolation and characterization of lactic [...] Read more.
The reported health effects of fermented dairy foods, which are traditionally manufactured in Bulgaria, are connected with their microbial biodiversity. The screening and development of probiotic starters for dairy products with unique properties are based exclusively on the isolation and characterization of lactic acid bacterial (LAB) strains. This study aims to systematically describe the LAB microbial content of artisanal products such as Bulgarian-type yoghurt, white brined cheese, kashkaval, koumiss, kefir, katak, and the Rhodope’s brano mliako. The original technologies for their preparation preserve the valuable microbial content and improve their nutritional and probiotic qualities. This review emphasises the features of LAB starters and the autochthonous microflora, the biochemistry of dairy food production, and the approaches for achieving the fortification of the foods with prebiotics, bioactive peptides (ACE2-inhibitors, bacteriocins, cyclic peptides with antimicrobial activity), immunomodulatory exopolysaccharides, and other metabolites (indol-3-propionic acid, free amino acids, antioxidants, prebiotics) with reported beneficial effects on human health. The link between the microbial content of dairy foods and the healthy human microbiome is highlighted. Full article
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